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LimmaStat

Select differentially expressed probesets, exons or transcripts from probeset, exon or transcript expression data by using limma statistical test.

Version 1.0
Bundle microarray
Categories Meap
Authors Ping Chen (ping.chen@helsinki.fi)
Issue tracker View/Report issues
Requires R ; meap (R-package)
Source files component.xml LimmaStat.r
Usage Example with default values

Inputs

Name Type Mandatory Description
expr LogMatrix Mandatory
sampleAnnotation CSV Mandatory

Outputs

Name Type Description
sigTarget CSV

Parameters

Name Type Default Description
IDcolumn int 1 The index of column that contains target IDs in 'expr'.
adjust string "BH" Method used to adjust the p-values for multiple testing. It can be one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr" or "none". A 'NULL' value will result in the default adjustment method, which is "BH".
contrasts string "" A common-separated string specifying contrasts. It is the same as the 'contrasts' used in limma \code{makeContrasts} function. For example, if we want to compare three groups 'A', 'B' and 'C', the 'contrasts' can be 'A-B,A-C,B-C'.
lfc float 0 Cutoff value for log2-fold-change. Only genes with larger fold changes are listed.
number int 100 Maximum number of genes to list.
pvalue float 2 Cutoff value for adjusted p-values. Only genes with lower p-values are listed.
sampleIDCol int 1 The index of column that contains sample IDs in 'sampleAnnotation'. The sample IDs should exist in column names of 'expr' matrix.
sampleType string "two.groups" A character string specifying the sample group types. It should be one of "two.groups","multi.groups","time.series" or "paired".
sortBy string "B" A string specifying statistic to rank genes by. It can be one of "logFC", "AveExpr", "t", "P", "B", or "none" when 'sampleType' is "two.groups" or "paired". It should be "F" or "none" when 'sampleType is "multi.groups" or "time.series".

Test cases

Test case Parameters IN
expr
IN
sampleAnnotation
OUT
sigTarget
case1 properties expr sampleAnnotation sigTarget

contrasts=wt-mu

case2 properties expr sampleAnnotation sigTarget

contrasts=C-A,C-T,A-T,
sampleType=multi.groups,
sortBy=F

case3 properties expr sampleAnnotation sigTarget

contrasts=t0-t6,t6-t12,t12-t36,
sampleType=time.series,
sortBy=F

case4 properties expr sampleAnnotation sigTarget

sampleType=paired


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