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<?xml version="1.0" encoding="UTF-8"?> |
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<!DOCTYPE part PUBLIC |
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philippe |
3 |
"-//Dawid Weiss//DTD DocBook V3.1-Based Extension for XML and graphics inclusion//EN" |
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"../../../../lib/docbook/preprocess/dweiss-docbook-extensions.dtd"> |
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5 |
<!-- |
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martin |
$Id: faqs.xml 3246 2007-04-16 14:12:23Z martin $ |
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7 |
|
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jari |
Copyright (C) 2007 Peter Johansson, Nicklas Nordborg, Philippe Rocca-Serra, Martin Svensson |
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06 Apr 09 |
nicklas |
Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg |
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|
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This file is part of BASE - BioArray Software Environment. |
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martin |
Available at http://base.thep.lu.se/ |
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13 |
|
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martin |
BASE is free software; you can redistribute it and/or |
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25 May 07 |
martin |
modify it under the terms of the GNU General Public License |
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05 Sep 08 |
jari |
as published by the Free Software Foundation; either version 3 |
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25 May 07 |
martin |
of the License, or (at your option) any later version. |
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25 May 07 |
martin |
18 |
|
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martin |
BASE is distributed in the hope that it will be useful, |
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25 May 07 |
martin |
but WITHOUT ANY WARRANTY; without even the implied warranty of |
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25 May 07 |
martin |
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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25 May 07 |
martin |
GNU General Public License for more details. |
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25 May 07 |
martin |
23 |
|
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25 May 07 |
martin |
You should have received a copy of the GNU General Public License |
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11 Sep 08 |
jari |
along with BASE. If not, see <http://www.gnu.org/licenses/>. |
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25 May 07 |
martin |
26 |
--> |
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24 May 07 |
philippe |
27 |
|
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jari |
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<part id="faqsdoc"> |
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<?dbhtml dir="faq" filename="index.html" ?> |
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26 Aug 08 |
jari |
30 |
<title>FAQ</title> |
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29 May 07 |
nicklas |
31 |
|
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26 Aug 08 |
jari |
32 |
<chapter id="faqs" chunked="0"> |
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04 Oct 11 |
nicklas |
33 |
<?dbhtml filename="faq.html" ?> |
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26 Aug 08 |
jari |
34 |
<title>Frequently Asked Questions with answers</title> |
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26 Aug 08 |
jari |
35 |
|
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26 Aug 08 |
jari |
36 |
<para> |
4416 |
26 Aug 08 |
jari |
37 |
This chapter presents a list of solutions to common problems and |
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26 Aug 08 |
jari |
38 |
tasks in BASE. The information is is collected from the mailing |
4416 |
26 Aug 08 |
jari |
39 |
lists, private communication, and from issues frequently |
4416 |
26 Aug 08 |
jari |
40 |
encountered in BASE introduction courses. If you have BASE |
4416 |
26 Aug 08 |
jari |
41 |
solutions that should be added to this chapter please contact us |
4416 |
26 Aug 08 |
jari |
42 |
through the usual communication channels, see |
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26 Aug 08 |
jari |
43 |
<xref linkend="resources" /> for contact information. |
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26 Aug 08 |
jari |
44 |
</para> |
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26 Aug 08 |
jari |
45 |
|
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26 Aug 08 |
jari |
46 |
<sect1 id="faqs.reporter"> |
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26 Aug 08 |
jari |
47 |
<title>Reporter related questions with answers</title> |
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25 May 07 |
martin |
48 |
<qandaset defaultlabel='qanda'> |
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29 May 07 |
nicklas |
49 |
<?dbhtml cellspacing="0px" cellpadding="0px" ?> |
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21 Aug 08 |
jari |
50 |
|
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25 May 07 |
martin |
51 |
<qandaentry> |
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25 May 07 |
martin |
52 |
<question> |
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25 May 07 |
martin |
53 |
<simpara> |
4402 |
21 Aug 08 |
jari |
54 |
My favourite database is not used for annotating reporters. Can I add |
4402 |
21 Aug 08 |
jari |
55 |
my database to BASE and if so, how should it proceed? |
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25 May 07 |
martin |
56 |
</simpara> |
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25 May 07 |
martin |
57 |
</question> |
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25 May 07 |
martin |
58 |
<answer> |
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25 May 07 |
martin |
59 |
<simpara> |
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29 May 07 |
nicklas |
60 |
Yes, you can add resources to annotate reporters. You will need to |
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21 Aug 08 |
jari |
61 |
upgrade BASE and you may have to contact your system administrator for |
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25 May 07 |
martin |
62 |
doing so. |
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25 May 07 |
martin |
63 |
</simpara> |
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24 May 07 |
philippe |
64 |
|
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25 May 07 |
martin |
65 |
<simpara> |
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29 May 07 |
nicklas |
66 |
In order to change, remove or add annotation fields attached to |
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29 May 07 |
nicklas |
67 |
reporters, you will need modify the <filename>extended-properties.xml</filename> |
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29 May 07 |
nicklas |
68 |
file and run a BASE update. Please refer to section |
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15 Sep 11 |
nicklas |
69 |
<xref linkend="installation.main" /> |
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25 May 07 |
martin |
70 |
for information about both processes. Once done with the upgrade, you'll |
4137 |
11 Feb 08 |
nicklas |
71 |
have to define a new reporter import plug-in. Instructions can be found |
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29 May 07 |
nicklas |
72 |
in <xref linkend="plugins" />. |
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25 May 07 |
martin |
73 |
</simpara> |
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25 May 07 |
martin |
74 |
</answer> |
3386 |
25 May 07 |
martin |
75 |
</qandaentry> |
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24 May 07 |
philippe |
76 |
|
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25 May 07 |
martin |
77 |
<qandaentry> |
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25 May 07 |
martin |
78 |
<question> |
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25 May 07 |
martin |
79 |
<simpara> |
3386 |
25 May 07 |
martin |
80 |
I have made a mistake while loading my reporters. How can I delete them |
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25 May 07 |
martin |
81 |
all in one go ? |
3386 |
25 May 07 |
martin |
82 |
</simpara> |
3386 |
25 May 07 |
martin |
83 |
</question> |
3386 |
25 May 07 |
martin |
84 |
<answer> |
3386 |
25 May 07 |
martin |
85 |
<simpara> |
4137 |
11 Feb 08 |
nicklas |
86 |
The reporter import plug-in can be executed in <emphasis>delete</emphasis> |
5682 |
02 Aug 11 |
nicklas |
87 |
mode. Run the plug-in again and select the same file you used for the import. |
4137 |
11 Feb 08 |
nicklas |
88 |
Select the <guilabel>Mode=delete</guilabel> option. |
4137 |
11 Feb 08 |
nicklas |
89 |
In the <guilabel>Error handling</guilabel> section select the |
4137 |
11 Feb 08 |
nicklas |
90 |
<guilabel>Reporter is used=skip</guilabel> option. This will delete all |
4137 |
11 Feb 08 |
nicklas |
91 |
reporters that was created in the previous import. |
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25 May 07 |
martin |
92 |
</simpara> |
3386 |
25 May 07 |
martin |
93 |
</answer> |
3386 |
25 May 07 |
martin |
94 |
</qandaentry> |
4403 |
21 Aug 08 |
jari |
95 |
|
4403 |
21 Aug 08 |
jari |
96 |
<qandaentry> |
4403 |
21 Aug 08 |
jari |
97 |
<question> |
4403 |
21 Aug 08 |
jari |
98 |
<simpara> |
4403 |
21 Aug 08 |
jari |
99 |
I get a message "Error: Unable to import root |
4403 |
21 Aug 08 |
jari |
100 |
bioassay. Item not found: |
5110 |
29 Sep 09 |
jari |
101 |
Reporter[externalId=AFFX-2315060]" when I try to create |
4403 |
21 Aug 08 |
jari |
102 |
a root bioassayset. |
4403 |
21 Aug 08 |
jari |
103 |
</simpara> |
4403 |
21 Aug 08 |
jari |
104 |
</question> |
4403 |
21 Aug 08 |
jari |
105 |
<answer> |
4403 |
21 Aug 08 |
jari |
106 |
<simpara> |
4403 |
21 Aug 08 |
jari |
107 |
BASE requires all reporters (probesets in Affymetrix |
4403 |
21 Aug 08 |
jari |
108 |
speak) to be stored in the database before they can be |
4403 |
21 Aug 08 |
jari |
109 |
used. The reporter information is typically imported |
4403 |
21 Aug 08 |
jari |
110 |
from a reporter annotation file but in some cases the |
4403 |
21 Aug 08 |
jari |
111 |
reporter annotation file supplied by Affymetrix fails to |
4403 |
21 Aug 08 |
jari |
112 |
describe all reporters (probesets) on a chip. BASE will |
4403 |
21 Aug 08 |
jari |
113 |
refuse to store data related to such chips until the |
4403 |
21 Aug 08 |
jari |
114 |
missing reporters are added to the database. Hence the |
4403 |
21 Aug 08 |
jari |
115 |
rejection of the new root bioassayset. |
4403 |
21 Aug 08 |
jari |
116 |
</simpara> |
4403 |
21 Aug 08 |
jari |
117 |
|
4403 |
21 Aug 08 |
jari |
118 |
<simpara> |
4403 |
21 Aug 08 |
jari |
119 |
The resolution is straightforward, simply import the |
4403 |
21 Aug 08 |
jari |
120 |
probeset information from the CDF file associated with |
4403 |
21 Aug 08 |
jari |
121 |
the array design. The catch is that normal BASE user |
4403 |
21 Aug 08 |
jari |
122 |
credential is not enough to perform the import therefore |
4403 |
21 Aug 08 |
jari |
123 |
someone with proper credential (the BASE server |
4403 |
21 Aug 08 |
jari |
124 |
administrator is one of them) must perform the |
4403 |
21 Aug 08 |
jari |
125 |
import. Follow the instructions at |
4403 |
21 Aug 08 |
jari |
126 |
<xref linkend="reporters.import" /> to import |
4403 |
21 Aug 08 |
jari |
127 |
reporters. Make sure to select plug-in option to ignore |
4403 |
21 Aug 08 |
jari |
128 |
already existing reporters when starting the import |
4403 |
21 Aug 08 |
jari |
129 |
otherwise the existing reporter annotations will be |
4403 |
21 Aug 08 |
jari |
130 |
changed. The goal here is to add missing reporters to |
4403 |
21 Aug 08 |
jari |
131 |
allow BASE work with your data. The CDF file does not |
4403 |
21 Aug 08 |
jari |
132 |
contain any annotation information and cannot be used to |
4403 |
21 Aug 08 |
jari |
133 |
annotate reporters. |
4403 |
21 Aug 08 |
jari |
134 |
</simpara> |
4403 |
21 Aug 08 |
jari |
135 |
</answer> |
4403 |
21 Aug 08 |
jari |
136 |
</qandaentry> |
4403 |
21 Aug 08 |
jari |
137 |
|
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25 May 07 |
martin |
138 |
</qandaset> |
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26 Aug 08 |
jari |
139 |
</sect1> |
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24 May 07 |
philippe |
140 |
|
4416 |
26 Aug 08 |
jari |
141 |
<sect1 id="faqs.arraydesign"> |
4416 |
26 Aug 08 |
jari |
142 |
<title>Array design related questions with answers</title> |
3386 |
25 May 07 |
martin |
143 |
<qandaset defaultlabel='qanda'> |
3402 |
29 May 07 |
nicklas |
144 |
<?dbhtml cellspacing="0px" cellpadding="0px" ?> |
3386 |
25 May 07 |
martin |
145 |
<qandaentry> |
3386 |
25 May 07 |
martin |
146 |
<question> |
3386 |
25 May 07 |
martin |
147 |
<para> |
4487 |
08 Sep 08 |
jari |
148 |
What it the best way to create an array design in BASE when starting |
3402 |
29 May 07 |
nicklas |
149 |
from a GAL file? |
3386 |
25 May 07 |
martin |
150 |
</para> |
3386 |
25 May 07 |
martin |
151 |
</question> |
3386 |
25 May 07 |
martin |
152 |
<answer> |
3386 |
25 May 07 |
martin |
153 |
<para> |
3402 |
29 May 07 |
nicklas |
154 |
This requires some work but here is the |
3386 |
25 May 07 |
martin |
155 |
procedure to remember: |
3386 |
25 May 07 |
martin |
156 |
</para> |
3386 |
25 May 07 |
martin |
157 |
<para> |
3402 |
29 May 07 |
nicklas |
158 |
A gal file tells where <guilabel>Reporters</guilabel> |
3402 |
29 May 07 |
nicklas |
159 |
have been spotted on an array. So a GAL file can be used to do 2 things |
3386 |
25 May 07 |
martin |
160 |
</para> |
3386 |
25 May 07 |
martin |
161 |
<orderedlist> |
3386 |
25 May 07 |
martin |
162 |
<listitem> |
3386 |
25 May 07 |
martin |
163 |
<para> |
4402 |
21 Aug 08 |
jari |
164 |
Define the features of an array design for a non-Affymetrix platform |
3402 |
29 May 07 |
nicklas |
165 |
using the <guilabel>Reporter Map importer plug-in</guilabel>. |
3386 |
25 May 07 |
martin |
166 |
</para> |
3386 |
25 May 07 |
martin |
167 |
<para> |
3402 |
29 May 07 |
nicklas |
168 |
To do so, after having created an new array design, go to the |
3402 |
29 May 07 |
nicklas |
169 |
single-item view by of the newly created array design. |
3402 |
29 May 07 |
nicklas |
170 |
Click on the &gbImport; |
3487 |
13 Jun 07 |
peter |
171 |
the button. If you do not see it, it means that you have not |
3402 |
29 May 07 |
nicklas |
172 |
enough privileges (contact the administrator). |
3386 |
25 May 07 |
martin |
173 |
</para> |
3386 |
25 May 07 |
martin |
174 |
<para> |
3402 |
29 May 07 |
nicklas |
175 |
This starts the plug-in configuration wizard. Select |
3402 |
29 May 07 |
nicklas |
176 |
the <guilabel>auto detect</guilabel> option and in the |
3402 |
29 May 07 |
nicklas |
177 |
next step your GAL file. |
3386 |
25 May 07 |
martin |
178 |
</para> |
3386 |
25 May 07 |
martin |
179 |
<para> |
3402 |
29 May 07 |
nicklas |
180 |
Now, there is the risk that no file format has been defined |
3402 |
29 May 07 |
nicklas |
181 |
for GAL files. This must be done by an administrator or other user |
3402 |
29 May 07 |
nicklas |
182 |
with proper privileges. See <xref linkend="plugins.configuration" /> |
4402 |
21 Aug 08 |
jari |
183 |
for information about this. |
3386 |
25 May 07 |
martin |
184 |
</para> |
3386 |
25 May 07 |
martin |
185 |
<para> |
3386 |
25 May 07 |
martin |
186 |
Once done (and if everything went fine), you can see from the |
3402 |
29 May 07 |
nicklas |
187 |
Array Design list view that the |
3386 |
25 May 07 |
martin |
188 |
<guilabel>Has features</guilabel> |
3386 |
25 May 07 |
martin |
189 |
entry has been modified and is set to 'Yes (n)' where n |
3402 |
29 May 07 |
nicklas |
190 |
indicates the number of spots (features) for this array. |
3386 |
25 May 07 |
martin |
191 |
</para> |
3386 |
25 May 07 |
martin |
192 |
<note> |
3386 |
25 May 07 |
martin |
193 |
<para> |
3402 |
29 May 07 |
nicklas |
194 |
Features can also be loaded from a Genepix GPR file |
3402 |
29 May 07 |
nicklas |
195 |
with the same procedure. |
3386 |
25 May 07 |
martin |
196 |
</para> |
3386 |
25 May 07 |
martin |
197 |
</note> |
3386 |
25 May 07 |
martin |
198 |
</listitem> |
3386 |
25 May 07 |
martin |
199 |
<listitem> |
3386 |
25 May 07 |
martin |
200 |
<para> |
3402 |
29 May 07 |
nicklas |
201 |
Define the |
3386 |
25 May 07 |
martin |
202 |
<guilabel>Reporters</guilabel> |
3402 |
29 May 07 |
nicklas |
203 |
present on the array design using the |
3402 |
29 May 07 |
nicklas |
204 |
<guilabel>Reporter importer plug-in</guilabel>. |
3386 |
25 May 07 |
martin |
205 |
</para> |
3386 |
25 May 07 |
martin |
206 |
<para> |
3402 |
29 May 07 |
nicklas |
207 |
To do so, Go to |
3402 |
29 May 07 |
nicklas |
208 |
<menuchoice> |
3402 |
29 May 07 |
nicklas |
209 |
<guimenu>View</guimenu> |
3402 |
29 May 07 |
nicklas |
210 |
<guimenuitem>Reporters</guimenuitem> |
3402 |
29 May 07 |
nicklas |
211 |
</menuchoice> |
3402 |
29 May 07 |
nicklas |
212 |
and click on |
3402 |
29 May 07 |
nicklas |
213 |
&gbImport;. This starts a |
3402 |
29 May 07 |
nicklas |
214 |
<guilabel>Reporter Importer plug-in</guilabel> |
3386 |
25 May 07 |
martin |
215 |
</para> |
3386 |
25 May 07 |
martin |
216 |
<para> |
3386 |
25 May 07 |
martin |
217 |
More information about importing Reporters can be found in |
3386 |
25 May 07 |
martin |
218 |
<xref linkend="reporters" /> |
3386 |
25 May 07 |
martin |
219 |
</para> |
3386 |
25 May 07 |
martin |
220 |
</listitem> |
3386 |
25 May 07 |
martin |
221 |
</orderedlist> |
3386 |
25 May 07 |
martin |
222 |
</answer> |
3386 |
25 May 07 |
martin |
223 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
224 |
|
3386 |
25 May 07 |
martin |
225 |
<qandaentry> |
3386 |
25 May 07 |
martin |
226 |
<question> |
3386 |
25 May 07 |
martin |
227 |
<para> |
3386 |
25 May 07 |
martin |
228 |
I am confused. What is the difference between |
3402 |
29 May 07 |
nicklas |
229 |
<guilabel>Reporter map importer</guilabel>, |
3402 |
29 May 07 |
nicklas |
230 |
<guilabel>Print map importer</guilabel> and |
3402 |
29 May 07 |
nicklas |
231 |
<guilabel>Reporter importer</guilabel>? |
3386 |
25 May 07 |
martin |
232 |
</para> |
3386 |
25 May 07 |
martin |
233 |
</question> |
3386 |
25 May 07 |
martin |
234 |
<answer> |
3386 |
25 May 07 |
martin |
235 |
<para> |
3402 |
29 May 07 |
nicklas |
236 |
The reporter map and print map importer are used to |
3402 |
29 May 07 |
nicklas |
237 |
import features to an array design. |
3402 |
29 May 07 |
nicklas |
238 |
The latter one must be used when your array design is connected to PCR |
3402 |
29 May 07 |
nicklas |
239 |
plates and supports two file formats: Biorobotics TAM |
3402 |
29 May 07 |
nicklas |
240 |
and Molecularware MWBR. See |
3402 |
29 May 07 |
nicklas |
241 |
<ulink url="http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php" |
3402 |
29 May 07 |
nicklas |
242 |
>http://www.flychip.org.uk/protocols/robotic_spotting/fileformats.php</ulink> |
3402 |
29 May 07 |
nicklas |
243 |
for more information about those file formats. |
4402 |
21 Aug 08 |
jari |
244 |
If you are only using commercial platforms or if you do not use plates in the array LIMS, you |
3402 |
29 May 07 |
nicklas |
245 |
have no need for the print map importer and should use the reporter |
3402 |
29 May 07 |
nicklas |
246 |
map importer instead. |
3386 |
25 May 07 |
martin |
247 |
</para> |
3372 |
24 May 07 |
philippe |
248 |
|
3386 |
25 May 07 |
martin |
249 |
<para> |
3402 |
29 May 07 |
nicklas |
250 |
The reporter importer is used to load reporter annotations into BASE. |
3386 |
25 May 07 |
martin |
251 |
</para> |
3386 |
25 May 07 |
martin |
252 |
</answer> |
3386 |
25 May 07 |
martin |
253 |
</qandaentry> |
3386 |
25 May 07 |
martin |
254 |
</qandaset> |
4416 |
26 Aug 08 |
jari |
255 |
</sect1> |
3372 |
24 May 07 |
philippe |
256 |
|
4416 |
26 Aug 08 |
jari |
257 |
<sect1 id="faqs.biomaterial"> |
4416 |
26 Aug 08 |
jari |
258 |
<title>Biomaterial, Protocol, Hardware, Software related questions with answers</title> |
3386 |
25 May 07 |
martin |
259 |
<qandaset defaultlabel='qanda'> |
3402 |
29 May 07 |
nicklas |
260 |
<?dbhtml cellspacing="0px" cellpadding="0px" ?> |
3386 |
25 May 07 |
martin |
261 |
<qandaentry> |
3386 |
25 May 07 |
martin |
262 |
<question> |
3386 |
25 May 07 |
martin |
263 |
<para> |
3402 |
29 May 07 |
nicklas |
264 |
I have just created a new item but I can not see |
3402 |
29 May 07 |
nicklas |
265 |
it. Am I doing something wrong? |
3386 |
25 May 07 |
martin |
266 |
</para> |
3386 |
25 May 07 |
martin |
267 |
</question> |
3386 |
25 May 07 |
martin |
268 |
<answer> |
3386 |
25 May 07 |
martin |
269 |
<para> |
3386 |
25 May 07 |
martin |
270 |
Try clearing the filter. To do so: use the |
3386 |
25 May 07 |
martin |
271 |
<guilabel>view / presets</guilabel> |
3386 |
25 May 07 |
martin |
272 |
dropdown and select the |
3386 |
25 May 07 |
martin |
273 |
<guilabel>clear filter</guilabel> |
3386 |
25 May 07 |
martin |
274 |
entry. This will remove all characters in the search boxes and all |
3386 |
25 May 07 |
martin |
275 |
preselection of item in the drop down lists. If this does not solve your |
3402 |
29 May 07 |
nicklas |
276 |
problem, then check if the <guilabel>view / presets</guilabel> |
3402 |
29 May 07 |
nicklas |
277 |
has the <guilabel>owned by me</guilabel> entry selected. |
3386 |
25 May 07 |
martin |
278 |
</para> |
3386 |
25 May 07 |
martin |
279 |
</answer> |
3386 |
25 May 07 |
martin |
280 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
281 |
|
3386 |
25 May 07 |
martin |
282 |
<qandaentry> |
3386 |
25 May 07 |
martin |
283 |
<question> |
3386 |
25 May 07 |
martin |
284 |
<para> |
3402 |
29 May 07 |
nicklas |
285 |
I can only see XX columns in the list view but I know I have |
4402 |
21 Aug 08 |
jari |
286 |
a lot more information. Is there a way I can customise the column |
3386 |
25 May 07 |
martin |
287 |
display? |
3386 |
25 May 07 |
martin |
288 |
</para> |
3386 |
25 May 07 |
martin |
289 |
</question> |
3386 |
25 May 07 |
martin |
290 |
<answer> |
3386 |
25 May 07 |
martin |
291 |
<para> |
3402 |
29 May 07 |
nicklas |
292 |
Yes, you can display many more columns. See <xref |
3402 |
29 May 07 |
nicklas |
293 |
linkend="webclient.itemlist.columns" />. |
3386 |
25 May 07 |
martin |
294 |
</para> |
3386 |
25 May 07 |
martin |
295 |
</answer> |
3386 |
25 May 07 |
martin |
296 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
297 |
|
3386 |
25 May 07 |
martin |
298 |
<qandaentry> |
3386 |
25 May 07 |
martin |
299 |
<question> |
3386 |
25 May 07 |
martin |
300 |
<para> |
3402 |
29 May 07 |
nicklas |
301 |
Is it possible to sort the values in a column in the list view? |
3386 |
25 May 07 |
martin |
302 |
</para> |
3386 |
25 May 07 |
martin |
303 |
</question> |
3386 |
25 May 07 |
martin |
304 |
<answer> |
3386 |
25 May 07 |
martin |
305 |
<para> |
3402 |
29 May 07 |
nicklas |
306 |
Of course it is. See <xref linkend="webclient.itemlist.order" />. |
3386 |
25 May 07 |
martin |
307 |
</para> |
3386 |
25 May 07 |
martin |
308 |
</answer> |
3386 |
25 May 07 |
martin |
309 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
310 |
|
3386 |
25 May 07 |
martin |
311 |
<qandaentry> |
3386 |
25 May 07 |
martin |
312 |
<question> |
3386 |
25 May 07 |
martin |
313 |
<para> |
3402 |
29 May 07 |
nicklas |
314 |
Is it possible to sort the annotation types from |
3402 |
29 May 07 |
nicklas |
315 |
<guilabel>Annotation & parameters</guilabel> tab in the |
3402 |
29 May 07 |
nicklas |
316 |
single-item view? |
3386 |
25 May 07 |
martin |
317 |
</para> |
3386 |
25 May 07 |
martin |
318 |
</question> |
3386 |
25 May 07 |
martin |
319 |
<answer> |
3402 |
29 May 07 |
nicklas |
320 |
<para> |
3402 |
29 May 07 |
nicklas |
321 |
No. This is not possible at the moment. The annotations are always sorted |
3402 |
29 May 07 |
nicklas |
322 |
by the name of the annotation type. |
3402 |
29 May 07 |
nicklas |
323 |
</para> |
3386 |
25 May 07 |
martin |
324 |
</answer> |
3386 |
25 May 07 |
martin |
325 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
326 |
|
3386 |
25 May 07 |
martin |
327 |
<qandaentry> |
3386 |
25 May 07 |
martin |
328 |
<question> |
3386 |
25 May 07 |
martin |
329 |
<para> |
3386 |
25 May 07 |
martin |
330 |
I have to create pools of samples in my experiment due to scarcity of |
4487 |
08 Sep 08 |
jari |
331 |
the biological material. Can I represent those pooled samples is BASE? |
3386 |
25 May 07 |
martin |
332 |
</para> |
3386 |
25 May 07 |
martin |
333 |
</question> |
3386 |
25 May 07 |
martin |
334 |
<answer> |
3386 |
25 May 07 |
martin |
335 |
<para> |
3402 |
29 May 07 |
nicklas |
336 |
Yes, you can. From the sample list select a number of samples |
3402 |
29 May 07 |
nicklas |
337 |
by marking their checkboxes. Then click on the <guibutton>Pool</guibutton> |
3402 |
29 May 07 |
nicklas |
338 |
button. For more information see |
5738 |
15 Sep 11 |
nicklas |
339 |
<xref linkend="biomaterial.samples.create" />. |
5682 |
02 Aug 11 |
nicklas |
340 |
Pooling can also be applied to extracts. |
3386 |
25 May 07 |
martin |
341 |
</para> |
3386 |
25 May 07 |
martin |
342 |
</answer> |
3386 |
25 May 07 |
martin |
343 |
</qandaentry> |
3386 |
25 May 07 |
martin |
344 |
<qandaentry> |
3386 |
25 May 07 |
martin |
345 |
<question> |
3386 |
25 May 07 |
martin |
346 |
<para> |
5682 |
02 Aug 11 |
nicklas |
347 |
I need to create a new item subtype but the |
3394 |
28 May 07 |
martin |
348 |
&gbNew; |
3386 |
25 May 07 |
martin |
349 |
button is grey and does not work. Why? |
3386 |
25 May 07 |
martin |
350 |
</para> |
3386 |
25 May 07 |
martin |
351 |
</question> |
3386 |
25 May 07 |
martin |
352 |
<answer> |
3386 |
25 May 07 |
martin |
353 |
<para> |
3402 |
29 May 07 |
nicklas |
354 |
Your privileges are not high enough and you have not been granted |
5682 |
02 Aug 11 |
nicklas |
355 |
permission to create subtypes. Contact your BASE administrator. |
3402 |
29 May 07 |
nicklas |
356 |
For more information about permissions, please refer to |
5738 |
15 Sep 11 |
nicklas |
357 |
<xref linkend="accounts" />. |
3386 |
25 May 07 |
martin |
358 |
</para> |
3386 |
25 May 07 |
martin |
359 |
</answer> |
3386 |
25 May 07 |
martin |
360 |
</qandaentry> |
3386 |
25 May 07 |
martin |
361 |
<qandaentry> |
3386 |
25 May 07 |
martin |
362 |
<question> |
3386 |
25 May 07 |
martin |
363 |
<para> |
3402 |
29 May 07 |
nicklas |
364 |
I have created an Annotation Type <userinput>Temperature</userinput> |
3402 |
29 May 07 |
nicklas |
365 |
and shared it to everyone but when I want to use it for annotating a |
3402 |
29 May 07 |
nicklas |
366 |
sample, I can not find it! How is that? |
3386 |
25 May 07 |
martin |
367 |
</para> |
3386 |
25 May 07 |
martin |
368 |
</question> |
3386 |
25 May 07 |
martin |
369 |
<answer> |
3386 |
25 May 07 |
martin |
370 |
<para> |
3402 |
29 May 07 |
nicklas |
371 |
The most likely explanation is that this particular annotation |
3402 |
29 May 07 |
nicklas |
372 |
type has been declared as a protocol parameter. This means that it will |
4487 |
08 Sep 08 |
jari |
373 |
only be displayed in BASE if you have used a sample creation protocol |
3402 |
29 May 07 |
nicklas |
374 |
which uses that parameter. |
3386 |
25 May 07 |
martin |
375 |
</para> |
3386 |
25 May 07 |
martin |
376 |
</answer> |
3386 |
25 May 07 |
martin |
377 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
378 |
|
3386 |
25 May 07 |
martin |
379 |
<qandaentry> |
3386 |
25 May 07 |
martin |
380 |
<question> |
3386 |
25 May 07 |
martin |
381 |
<para> |
3386 |
25 May 07 |
martin |
382 |
I have carried out an experiment using both Affymetrix and Agilent |
4487 |
08 Sep 08 |
jari |
383 |
arrays but I can not select more than one raw data type in BASE. What |
3402 |
29 May 07 |
nicklas |
384 |
should I do? |
3386 |
25 May 07 |
martin |
385 |
</para> |
3386 |
25 May 07 |
martin |
386 |
</question> |
3386 |
25 May 07 |
martin |
387 |
<answer> |
3386 |
25 May 07 |
martin |
388 |
<para> |
3386 |
25 May 07 |
martin |
389 |
In this particular case and because you are using 2 different raw data |
3386 |
25 May 07 |
martin |
390 |
file formats, you will have to split your experiment in 2. One |
3386 |
25 May 07 |
martin |
391 |
experiment for those samples processed using Affymetrix platform and |
3487 |
13 Jun 07 |
peter |
392 |
another one using Agilent platform. You do not necessarily have to |
3386 |
25 May 07 |
martin |
393 |
provide all information about the samples again but simply create new |
3386 |
25 May 07 |
martin |
394 |
raw bioassay data which can be grouped in a new experiment. |
3386 |
25 May 07 |
martin |
395 |
</para> |
3386 |
25 May 07 |
martin |
396 |
</answer> |
3386 |
25 May 07 |
martin |
397 |
</qandaentry> |
3386 |
25 May 07 |
martin |
398 |
</qandaset> |
4416 |
26 Aug 08 |
jari |
399 |
</sect1> |
3372 |
24 May 07 |
philippe |
400 |
|
4416 |
26 Aug 08 |
jari |
401 |
<sect1 id="faqs.datafiles_rawdata"> |
4416 |
26 Aug 08 |
jari |
402 |
<title>Data Files and Raw Data related questions with answers</title> |
3386 |
25 May 07 |
martin |
403 |
<qandaset defaultlabel='qanda'> |
3402 |
29 May 07 |
nicklas |
404 |
<?dbhtml cellspacing="0px" cellpadding="0px" ?> |
3386 |
25 May 07 |
martin |
405 |
<qandaentry> |
3386 |
25 May 07 |
martin |
406 |
<question> |
3386 |
25 May 07 |
martin |
407 |
<para> |
4487 |
08 Sep 08 |
jari |
408 |
It seems that BASE does not support the data files generated by my brand |
4487 |
08 Sep 08 |
jari |
409 |
new scanner. Is it possible to add it to BASE? |
3386 |
25 May 07 |
martin |
410 |
</para> |
3386 |
25 May 07 |
martin |
411 |
</question> |
3386 |
25 May 07 |
martin |
412 |
<answer> |
3386 |
25 May 07 |
martin |
413 |
<para> |
4487 |
08 Sep 08 |
jari |
414 |
Yes it is possible to extend BASE so that it can support your system. |
4487 |
08 Sep 08 |
jari |
415 |
You will need to define a new raw data type for BASE by modifying |
3402 |
29 May 07 |
nicklas |
416 |
the <filename>raw-datatypes.xml</filename> configuration file. |
3386 |
25 May 07 |
martin |
417 |
</para> |
3386 |
25 May 07 |
martin |
418 |
<para> |
3402 |
29 May 07 |
nicklas |
419 |
Then, you will have to run the <filename>updatedb.sh</filename> |
3402 |
29 May 07 |
nicklas |
420 |
to make the new raw data type available to the system. See |
5738 |
15 Sep 11 |
nicklas |
421 |
<xref linkend="installation.upgrade" />. |
3386 |
25 May 07 |
martin |
422 |
</para> |
3386 |
25 May 07 |
martin |
423 |
<para> |
3402 |
29 May 07 |
nicklas |
424 |
Finally, you will have to configure a raw data import plug-in in order to |
3402 |
29 May 07 |
nicklas |
425 |
be able to create rawbioassays. See |
3386 |
25 May 07 |
martin |
426 |
<xref linkend="plugins.configuration" /> |
3386 |
25 May 07 |
martin |
427 |
and |
3402 |
29 May 07 |
nicklas |
428 |
<xref linkend="experiments_analysis.rawbioassay.rawdata" /> |
3386 |
25 May 07 |
martin |
429 |
for further information. |
3386 |
25 May 07 |
martin |
430 |
</para> |
3386 |
25 May 07 |
martin |
431 |
</answer> |
3386 |
25 May 07 |
martin |
432 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
433 |
|
3386 |
25 May 07 |
martin |
434 |
<qandaentry> |
3386 |
25 May 07 |
martin |
435 |
<question> |
4487 |
08 Sep 08 |
jari |
436 |
<para>Are Affymetrix CDT and CAB files supported by BASE?</para> |
3386 |
25 May 07 |
martin |
437 |
</question> |
3386 |
25 May 07 |
martin |
438 |
<answer> |
3386 |
25 May 07 |
martin |
439 |
<para> |
3402 |
29 May 07 |
nicklas |
440 |
There is no support for CDT or CAB. Currently only CDF and CEL files are |
3386 |
25 May 07 |
martin |
441 |
supported by the Affymetrix plug-ins. Annotation files (.csv) are used |
3386 |
25 May 07 |
martin |
442 |
for uploading probeset (reporter in BASE language) information. The |
3402 |
29 May 07 |
nicklas |
443 |
issue of supporting CDT and CAB files is an import and a plug-in issue. |
3402 |
29 May 07 |
nicklas |
444 |
There are two ways to solve this: |
3402 |
29 May 07 |
nicklas |
445 |
<orderedlist> |
3402 |
29 May 07 |
nicklas |
446 |
<listitem> |
3402 |
29 May 07 |
nicklas |
447 |
<para> |
3402 |
29 May 07 |
nicklas |
448 |
Write code that treats the files in a proper way and submit |
3402 |
29 May 07 |
nicklas |
449 |
the solution to the developer team (preferred route). |
3402 |
29 May 07 |
nicklas |
450 |
</para> |
3402 |
29 May 07 |
nicklas |
451 |
</listitem> |
3402 |
29 May 07 |
nicklas |
452 |
<listitem> |
3402 |
29 May 07 |
nicklas |
453 |
<para> |
3402 |
29 May 07 |
nicklas |
454 |
Submit a ticket through |
7982 |
14 Jun 21 |
nicklas |
455 |
<ulink url="https://base.thep.lu.se">https://base.thep.lu.se</ulink> |
3402 |
29 May 07 |
nicklas |
456 |
explaining what you'd like to see with respect to to CDT and CAB files. |
3402 |
29 May 07 |
nicklas |
457 |
</para> |
3402 |
29 May 07 |
nicklas |
458 |
</listitem> |
3402 |
29 May 07 |
nicklas |
459 |
</orderedlist> |
3402 |
29 May 07 |
nicklas |
460 |
|
3402 |
29 May 07 |
nicklas |
461 |
<note> |
3402 |
29 May 07 |
nicklas |
462 |
<para> |
3402 |
29 May 07 |
nicklas |
463 |
To include CDT and CAB support to BASE, the file formats must be |
3402 |
29 May 07 |
nicklas |
464 |
open, that is we must be able to read them without proprietary |
3402 |
29 May 07 |
nicklas |
465 |
non-distributable code. |
3402 |
29 May 07 |
nicklas |
466 |
</para> |
3402 |
29 May 07 |
nicklas |
467 |
</note> |
3386 |
25 May 07 |
martin |
468 |
</para> |
3386 |
25 May 07 |
martin |
469 |
</answer> |
3386 |
25 May 07 |
martin |
470 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
471 |
|
3386 |
25 May 07 |
martin |
472 |
<qandaentry> |
3386 |
25 May 07 |
martin |
473 |
<question> |
4487 |
08 Sep 08 |
jari |
474 |
<para>Are Illumina data files supported by BASE?</para> |
3386 |
25 May 07 |
martin |
475 |
</question> |
3386 |
25 May 07 |
martin |
476 |
<answer> |
3386 |
25 May 07 |
martin |
477 |
<para> |
4452 |
05 Sep 08 |
jari |
478 |
Yes, but not by default. There is |
7982 |
14 Jun 21 |
nicklas |
479 |
an <ulink url="https://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina">Illumina |
4452 |
05 Sep 08 |
jari |
480 |
package</ulink> that provides Illumina support to |
4452 |
05 Sep 08 |
jari |
481 |
BASE. The package is straightforward to install, visit |
4452 |
05 Sep 08 |
jari |
482 |
the package site for more information. |
3386 |
25 May 07 |
martin |
483 |
</para> |
3386 |
25 May 07 |
martin |
484 |
</answer> |
3386 |
25 May 07 |
martin |
485 |
</qandaentry> |
4452 |
05 Sep 08 |
jari |
486 |
|
3386 |
25 May 07 |
martin |
487 |
</qandaset> |
4452 |
05 Sep 08 |
jari |
488 |
|
4416 |
26 Aug 08 |
jari |
489 |
</sect1> |
3372 |
24 May 07 |
philippe |
490 |
|
3372 |
24 May 07 |
philippe |
491 |
|
4416 |
26 Aug 08 |
jari |
492 |
<sect1 id="faqs.analysis"> |
4416 |
26 Aug 08 |
jari |
493 |
<title>Analysis related questions with answers</title> |
3386 |
25 May 07 |
martin |
494 |
<qandaset defaultlabel='qanda'> |
3402 |
29 May 07 |
nicklas |
495 |
<?dbhtml cellspacing="0px" cellpadding="0px" ?> |
3386 |
25 May 07 |
martin |
496 |
<qandaentry> |
3386 |
25 May 07 |
martin |
497 |
<question> |
3386 |
25 May 07 |
martin |
498 |
<para> |
3402 |
29 May 07 |
nicklas |
499 |
Is it possible to use the formula filter to filter for |
3402 |
29 May 07 |
nicklas |
500 |
<constant>null</constant> |
3402 |
29 May 07 |
nicklas |
501 |
values (or non-<constant>null</constant> values)? |
3386 |
25 May 07 |
martin |
502 |
</para> |
3386 |
25 May 07 |
martin |
503 |
</question> |
3386 |
25 May 07 |
martin |
504 |
<answer> |
3402 |
29 May 07 |
nicklas |
505 |
<para> |
5682 |
02 Aug 11 |
nicklas |
506 |
Yes, use an expression like: |
5682 |
02 Aug 11 |
nicklas |
507 |
<userinput>ch(0) != null</userinput>. This will match |
4402 |
21 Aug 08 |
jari |
508 |
all values, except <constant>null</constant> values. |
3402 |
29 May 07 |
nicklas |
509 |
</para> |
3386 |
25 May 07 |
martin |
510 |
</answer> |
3386 |
25 May 07 |
martin |
511 |
</qandaentry> |
3372 |
24 May 07 |
philippe |
512 |
|
3386 |
25 May 07 |
martin |
513 |
<qandaentry> |
3386 |
25 May 07 |
martin |
514 |
<question> |
3386 |
25 May 07 |
martin |
515 |
<para> |
4487 |
08 Sep 08 |
jari |
516 |
OK, I have uploaded 40 CEL files in BASE but are there any tool to |
4402 |
21 Aug 08 |
jari |
517 |
perform normalisation on Affymetrix raw data? |
3386 |
25 May 07 |
martin |
518 |
</para> |
3386 |
25 May 07 |
martin |
519 |
</question> |
3386 |
25 May 07 |
martin |
520 |
<answer> |
3386 |
25 May 07 |
martin |
521 |
<para> |
4487 |
08 Sep 08 |
jari |
522 |
Yes, there is. BASE team has created a plug-in based on |
3402 |
29 May 07 |
nicklas |
523 |
<ulink url="http://rmaexpress.bmbolstad.com/"> |
4402 |
21 Aug 08 |
jari |
524 |
RMAExpress methods from Bolstad and Irizarry</ulink> so you can normalise |
4402 |
21 Aug 08 |
jari |
525 |
Affymetrix data sets of reasonable size (not 1000 CEL files at a time |
3386 |
25 May 07 |
martin |
526 |
though even though this might depend on your set-up...) |
3402 |
29 May 07 |
nicklas |
527 |
The plug-in is not included in a standard BASE installation, but |
7982 |
14 Jun 21 |
nicklas |
528 |
can be downloaded from the <ulink url="https://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix" |
3402 |
29 May 07 |
nicklas |
529 |
>BASE plug-ins web site</ulink>. |
3386 |
25 May 07 |
martin |
530 |
</para> |
3386 |
25 May 07 |
martin |
531 |
</answer> |
3386 |
25 May 07 |
martin |
532 |
</qandaentry> |
5110 |
29 Sep 09 |
jari |
533 |
|
5110 |
29 Sep 09 |
jari |
534 |
<qandaentry> |
5110 |
29 Sep 09 |
jari |
535 |
<question> |
5110 |
29 Sep 09 |
jari |
536 |
<para> |
5110 |
29 Sep 09 |
jari |
537 |
I am trying to import raw bioassays using the import |
5110 |
29 Sep 09 |
jari |
538 |
button in the experiment properties view but BASE claims |
5110 |
29 Sep 09 |
jari |
539 |
that <emphasis>Could not find any plugins that you have |
5110 |
29 Sep 09 |
jari |
540 |
permission to use</emphasis>. I know there are import |
5110 |
29 Sep 09 |
jari |
541 |
plug-ins available to me since I have successfully |
5110 |
29 Sep 09 |
jari |
542 |
imported data before, why does the import fail? |
5110 |
29 Sep 09 |
jari |
543 |
</para> |
5110 |
29 Sep 09 |
jari |
544 |
</question> |
5110 |
29 Sep 09 |
jari |
545 |
<answer> |
5110 |
29 Sep 09 |
jari |
546 |
<para> |
5110 |
29 Sep 09 |
jari |
547 |
All raw bioassays in the experiment are already |
5110 |
29 Sep 09 |
jari |
548 |
imported. In this case the BASE server cannot detect |
5110 |
29 Sep 09 |
jari |
549 |
anything to import and returns the somewhat confusing |
5110 |
29 Sep 09 |
jari |
550 |
message. Simply add the non-imported raw bioassays to |
5110 |
29 Sep 09 |
jari |
551 |
the experiment and try again. |
5110 |
29 Sep 09 |
jari |
552 |
</para> |
5110 |
29 Sep 09 |
jari |
553 |
</answer> |
5110 |
29 Sep 09 |
jari |
554 |
</qandaentry> |
3386 |
25 May 07 |
martin |
555 |
</qandaset> |
4416 |
26 Aug 08 |
jari |
556 |
</sect1> |
4416 |
26 Aug 08 |
jari |
557 |
|
4416 |
26 Aug 08 |
jari |
558 |
</chapter> |
4416 |
26 Aug 08 |
jari |
559 |
|
3386 |
25 May 07 |
martin |
560 |
</part> |