SAM.DiffExpress: Use SAM for Differential Expression

In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

Use SAM for Differential Expression

Description

Use the SAM method to find differentially expressed genes from a set of transcriptome files.

Usage

SAM.DiffExpress(fnames, fids, groupset, targetGroup = sort(groupset)[1], 
		geneColumn = "GENE_ID", intensityColumn = "INTENSITY", 
		keepIntergenics = FALSE, minimumIntensity = NULL, 
		missingGenes = "fill", 
		wt.folds = 1, wt.pvalues = 1, wt.dists = 1, ...)

Arguments

fnames	character vector of full pathnames to existing transcriptome files
fids	character vector of SampleIDs
groupset	character vector of GroupIDs or conditions, to categorize the transcripts
targetGroup	the one GroupID to be the chosen subset, to compare all other groups against. This is the group that is being tested for up-regulation.
geneColumn	column name of the column of GeneIDs
intensityColumn	column name of the column of intensity values
keepIntergenics	logical, explicity keep the non-genes, or drop them from consideration
minimumIntensity	the 'fudge factor' called 'S0' for SAM, that represents a minimum intensity added to all denominators to prevent division by zero and effectively scale the distances 'D' produced by SAM
missingGenes	method for dealing with genes that are not present in every transcript file. Either drop entire gene rows, or fill in with minimum observed intensity.
wt.folds, wt.pvalues, wt.dists	weight terms for influencing the final ordering of DE genes. See SAM.diffExpressRankOrder

Details

This function implements the SAM algorithm of Tusher, et.al., as implemented in R package 'siggenes' by H. Schwender.

Value

A data frame of consensus gene differential expression, sorted by consensus of up-regulation, with columns:

GENE_ID	the genes, sorted from most up-regulated to most down-regulated
PRODUCT	the gene product descriptions
LOG_2_FOLD	the average fold change for each gene
P_VALUE	the P-value for each gene
Q_VALUE	the Q-value for each gene
AVG_SET1	the average gene intensity over all samples in group targetGroup
AVG_SET2	the average gene intensity over all samples in the other groups

Note

Typically, this function is called once for each group, to get all possible DE comparisons between the various groups. While the function explicitly measures up-regulation, by reversing the order of the rows of the result, you get the answer for down-regulation.

Author(s)

Bob Morrison

References

V. Tusher, et.al., PNAS 98 (2001)

See Also

rankProductDiffExpress, for the Rank Product method.

robertdouglasmorrison/DuffyTools documentation built on April 13, 2025, 8:51 p.m.