2 |
26 Feb 07 |
jari |
1 |
<html> |
2 |
26 Feb 07 |
jari |
2 |
<body bgcolor = "#FFFFCC"> |
2 |
26 Feb 07 |
jari |
3 |
<basefont face = "Arial" padding=10> |
2 |
26 Feb 07 |
jari |
4 |
<h1>BRIDGE - Bayesion Robust Inference of Differential Gene Expression</h1> |
2 |
26 Feb 07 |
jari |
5 |
<h1>Bridge Initialization Dialog</h1> |
2 |
26 Feb 07 |
jari |
6 |
<hr size = 1> |
2 |
26 Feb 07 |
jari |
7 |
|
2 |
26 Feb 07 |
jari |
8 |
<h2>Bridge</h2> |
2 |
26 Feb 07 |
jari |
9 |
The bridge package consists of several functions for testing for differential expression |
2 |
26 Feb 07 |
jari |
10 |
among multiple samples. |
2 |
26 Feb 07 |
jari |
11 |
|
2 |
26 Feb 07 |
jari |
12 |
<h2>Data Type</h2> |
2 |
26 Feb 07 |
jari |
13 |
The type of data that was loaded |
2 |
26 Feb 07 |
jari |
14 |
<br><br> |
2 |
26 Feb 07 |
jari |
15 |
If the data is affy, but was not loaded through the affy loader, choose "Intensity Data". This is |
2 |
26 Feb 07 |
jari |
16 |
allows users to export Affy data from GCOS or GCRMA as text files and load them into MeV. |
2 |
26 Feb 07 |
jari |
17 |
<br><br> |
2 |
26 Feb 07 |
jari |
18 |
|
2 |
26 Feb 07 |
jari |
19 |
<h2> Experiment Labeling </h2> |
2 |
26 Feb 07 |
jari |
20 |
Each slide (experiment or hyb) loaded into MeV is listed here. You must tell Rama how you've |
2 |
26 Feb 07 |
jari |
21 |
labeled your samples. |
2 |
26 Feb 07 |
jari |
22 |
<br><br> |
2 |
26 Feb 07 |
jari |
23 |
If you've loaded 2 color data, you are asked to indicate which color ( Cy3 or Cy5 ) dye was |
2 |
26 Feb 07 |
jari |
24 |
used on your control samples. It is assumed that the other was used for the treated sample |
2 |
26 Feb 07 |
jari |
25 |
on that slide. Bridge will infer from the labeling whether or not your experiment was dye-swapped |
2 |
26 Feb 07 |
jari |
26 |
based on your input here. Keep in mind that Rama requires at least 2 of any color data. |
2 |
26 Feb 07 |
jari |
27 |
<br><br> |
2 |
26 Feb 07 |
jari |
28 |
|
2 |
26 Feb 07 |
jari |
29 |
<h2>Advanced Parameters</h2> |
2 |
26 Feb 07 |
jari |
30 |
# Iterations ( B ) - the number of iterations used by Bridge |
2 |
26 Feb 07 |
jari |
31 |
<br><br> |
2 |
26 Feb 07 |
jari |
32 |
Burn In Period ( num.iter ) - the length of the burn-in period in the MCMC algorithm. This |
2 |
26 Feb 07 |
jari |
33 |
should be less than # Iterations ( B ) |
2 |
26 Feb 07 |
jari |
34 |
<br><br> |
2 |
26 Feb 07 |
jari |
35 |
|
2 |
26 Feb 07 |
jari |
36 |
<h2>Rserve</h2> |
2 |
26 Feb 07 |
jari |
37 |
This implementation has been built allow the user to connect to any Rserve daemon. Upon |
2 |
26 Feb 07 |
jari |
38 |
load, the pull down menu is populated with the connection strings from the config file |
2 |
26 Feb 07 |
jari |
39 |
( config/tmev.cfg ). The user can add a new connection string here if desired. |
2 |
26 Feb 07 |
jari |
40 |
<br><br> |
2 |
26 Feb 07 |
jari |
41 |
The format is: ipaddress:port. |
2 |
26 Feb 07 |
jari |
42 |
<br><br> |
2 |
26 Feb 07 |
jari |
43 |
For example, if the server running Rserve is at IP address 192.168.0.1 and |
2 |
26 Feb 07 |
jari |
44 |
Rserve is running on its default port ( 6311 ), the connection string would be 192.168.0.1:6311. |
2 |
26 Feb 07 |
jari |
45 |
The user can type that into the text field, click add, make sure it is selected in the pull down |
2 |
26 Feb 07 |
jari |
46 |
menu and then run Bridge. If the connection was made without any errors, the new connection |
2 |
26 Feb 07 |
jari |
47 |
string will be added automatically to the config file. Of course, the user always has the option |
2 |
26 Feb 07 |
jari |
48 |
of manually adding/editing the connection strings in the config file. |
2 |
26 Feb 07 |
jari |
49 |
<br><br> |
2 |
26 Feb 07 |
jari |
50 |
See http://www.expression.washington.edu/ramaDoc/MeV-R_Documentation.html for more details |
2 |
26 Feb 07 |
jari |
51 |
</basefont> |
2 |
26 Feb 07 |
jari |
52 |
</body> |
2 |
26 Feb 07 |
jari |
53 |
</html> |