FDR for PLPE

Description

This computes FDR for PLPE.

Usage

1

Arguments

x

data matrix

...

other arguments

Author(s)

HyungJun Cho and Jae K. Lee

References

Cho H, Smalley DM, Ross MM, Theodorescu D, Ley K and Lee JK (2007). Statistical Identification of Differentially Labelled Peptides from Liquid Chromatography Tandem Mass Spectrometry, Proteomics, 7:3681-3692.

See Also

lpe.paired.fdr.default

Examples

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#LC-MS/MS proteomic data for platelets MPs
library(PLPE)
data(plateletSet)
x <- exprs(plateletSet)
x <- log2(x) 

cond <- c(1, 2, 1, 2, 1, 2)
pair <- c(1, 1, 2, 2, 3, 3)
design <- cbind(cond, pair)

out <- lpe.paired(x, design, q=0.1, data.type="ms")
out.fdr <- lpe.paired.fdr(x,obj=out)
out.fdr$FDR[1:10,]