fdrSAM

Description

Calculate the false discovery rate (FDR) by permutation for the group differences as calculated by SAM.

Usage

1
  fdrSAM(G, y, nperms, tt.sam, alternative = "two.sided")

Arguments

G

Matrix of gene expression, columns ordered in the same order at the cell-frequency matrix (n by g, n samples, g genes)

y

A numeric vector of group association of each sample. Either 1 or 2.

nperms

Number of permutations to run. User responsability to the number appropriately fitting the sample size.

tt.sam

Real group comparison t-test statistic value

alternative

Type of test. Choices are 'two.sided','greater' or 'less'

Value

A list

fdr.sam

A vector false dicovery rates for SAM comparison at different thresholds. A set of 100 theresholds is determined automatically from the data.

ncall.sam

Number of genes called significant at the given cutoff threshold with a FDR matching that indicated in fdr.sam

ttstar.sam

A matrix listing the t statistic for each gene in each permutation. (p by g, p permutations, g genes)

sigGene.sam

A vector of length equal to the number of genes being considered. For each gene the estimated FDR is listed.

Author(s)

Shai Shen-Orr, Rob Tibshirani, Narasimhan Balasubramanian, David Wang

References

Shen-Orr SS, Tibshirani R, Khatri P, Bodian DL, Staedtler F, Perry NM, Hastie T, Sarwal MM, Davis MM and Butte AJ (2010). "Cell type-specific gene expression differences in complex tissues." _Nature methods_, *7*(4), pp. 287-9. ISSN 1548-7105, <URL: http://dx.doi.org/10.1038/nmeth.1439>, <URL: http://www.ncbi.nlm.nih.gov/pubmed/20208531>.