Up: Component summary
Up: Component summary
Component
LimmaStatSelect 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 |
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|---|---|---|---|---|---|---|
| case1 | properties | expr | sampleAnnotation | sigTarget | ||
|
contrasts=wt-mu |
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| case2 | properties | expr | sampleAnnotation | sigTarget | ||
|
contrasts=C-A,C-T,A-T, |
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| case3 | properties | expr | sampleAnnotation | sigTarget | ||
|
contrasts=t0-t6,t6-t12,t12-t36, |
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| case4 | properties | expr | sampleAnnotation | sigTarget | ||
|
sampleType=paired |
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