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enell |
BASEfile |
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enell |
section plugin |
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enell |
uniqueName onk.lu.se/enell/ReplicateError |
| 771 |
18 Sep 08 |
jari |
versionNumber @VERSION@ |
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enell |
name Filter: ReplicateError (within assays) |
| 2015 |
02 Aug 13 |
olle |
descr Implementation of 'Analysis of replicates' (cf. figure 4 in the publication)\r\nWithin the fold: assessing differential expression measures and reproducibility in microarray assays.\r\nYang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062. Epub 2002 Oct 24.\r\n\r\nParameters:\r\n\r\nStandard deviation limit - Filters out values outside the limit. A limit value <= 0 indicates that no limit is used.\r\n\r\nLeave singletons - Flag indicating if spots occurring once should be leaved.\r\n\r\nCenter of mass - median (default) or mean |
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enell |
execName runWA |
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enell |
geneAverages 0 |
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enell |
serialFormat 0 |
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enell |
url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12429061 |
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enell |
minChannels 2 |
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enell |
maxChannels 0 |
| 46 |
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enell |
leaveStdin 0 |
| 46 |
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enell |
leaveStdout 0 |
| 46 |
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enell |
estimatedTime 60 |
| 46 |
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enell |
defaultMaxRam 67108864 |
| 46 |
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enell |
usedColumns position\treporter |
| 46 |
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enell |
usedFields _allIntensities |
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enell |
columns position valueType name commonName options defaultValue enumOptions removed |
| 46 |
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enell |
20 |
% |
| 766 |
16 Sep 08 |
jari |
1 e strictReplicate Replicate filter 30 true true\ton\tfalse\toff 1 |
| 766 |
16 Sep 08 |
jari |
2 h section 30 settings 0 |
| 766 |
16 Sep 08 |
jari |
3 f sdLimit Standard deviation limit 30 2.0 0 |
| 766 |
16 Sep 08 |
jari |
4 e newBAS Create new bioassay set 30 true true\tyes\tfalse\tno 1 |
| 766 |
16 Sep 08 |
jari |
5 e leaveSingletons Leave singletons 30 false true\tyes\tfalse\tno 0 |
| 766 |
16 Sep 08 |
jari |
6 e leaveDataFiles Put gnuplot file in zip archive 30 false true\tyes\tfalse\tno 1 |
| 766 |
16 Sep 08 |
jari |
7 e method Method 30 1 1\tSD Limit\t2\tmin(ch1, ch2)\t3\t### 1 |
| 766 |
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jari |
8 f startvalue Start value 30 1 |
| 766 |
16 Sep 08 |
jari |
9 f stepSize Step size 30 1 |
| 766 |
16 Sep 08 |
jari |
10 f rTarget R target 30 0.95 1 |
| 766 |
16 Sep 08 |
jari |
11 e center Center of mass 30 0 0\tMedian\t1\tMean 0 |
| 46 |
22 Nov 05 |
enell |
32 |
|