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Last change
on this file since 2015 was
2015,
checked in by olle, 9 years ago
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Refs #84. ReplicateError BASE1 plug-in configuration file lib/pluginConfigurationWA.base updated in parameter info, as the previous update erroneously included parameters used by ReplicateErrorAA, but not by ReplicateErrorWA.
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-
Property svn:eol-style set to
native
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File size:
1.6 KB
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| 1 | BASEfile |
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| 2 | section plugin |
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| 3 | uniqueName onk.lu.se/enell/ReplicateError |
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| 4 | versionNumber @VERSION@ |
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| 5 | name Filter: ReplicateError (within assays) |
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| 6 | 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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| 7 | execName runWA |
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| 8 | geneAverages 0 |
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| 9 | serialFormat 0 |
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| 10 | url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12429061 |
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| 11 | minChannels 2 |
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| 12 | maxChannels 0 |
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| 13 | leaveStdin 0 |
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| 14 | leaveStdout 0 |
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| 15 | estimatedTime 60 |
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| 16 | defaultMaxRam 67108864 |
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| 17 | usedColumns position\treporter |
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| 18 | usedFields _allIntensities |
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| 19 | columns position valueType name commonName options defaultValue enumOptions removed |
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| 20 | % |
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| 21 | 1 e strictReplicate Replicate filter 30 true true\ton\tfalse\toff 1 |
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| 22 | 2 h section 30 settings 0 |
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| 23 | 3 f sdLimit Standard deviation limit 30 2.0 0 |
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| 24 | 4 e newBAS Create new bioassay set 30 true true\tyes\tfalse\tno 1 |
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| 25 | 5 e leaveSingletons Leave singletons 30 false true\tyes\tfalse\tno 0 |
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| 26 | 6 e leaveDataFiles Put gnuplot file in zip archive 30 false true\tyes\tfalse\tno 1 |
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| 27 | 7 e method Method 30 1 1\tSD Limit\t2\tmin(ch1, ch2)\t3\t### 1 |
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| 28 | 8 f startvalue Start value 30 1 |
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| 29 | 9 f stepSize Step size 30 1 |
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| 30 | 10 f rTarget R target 30 0.95 1 |
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| 31 | 11 e center Center of mass 30 0 0\tMedian\t1\tMean 0 |
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| 32 | |
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