Local Pooled Error Test for Paired Data

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Description

This invetigates differential expression for paired high-throughput data.

Usage

1

Arguments

x

an object for which the extraction of model lpe.paired is meaningful.

...

other arguments

Value

x

design matrix; condition index in the first column and pair index in the sceond column

...

data type: 'ms' for mass spectrometry data, 'cdna' for cDNA microarray data

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.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$test.out[1:10,]