psmeans: Function to take means of probesets.

In LMGene: LMGene Software for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays

Description

Converts an ExpressionSet or AffyBatch object with one row of expression data per probeset into an ExpressionSet or AffyBatch object with one row per probe.

Usage

psmeans(eS, ind)

Arguments

eS	An ExpressionSet or AffyBatch object
ind	A vector used to indicate which probes go into which probesets.

Details

Each entry of ind corresponds to one probe and tells the number of the probeset it belongs to. See tranestAffyProbeLevel and sample.ind for examples.

Value

Returns an ExpressionSet or AffyBatch object with the expression matrix rows corresponding to probesets instead of individual probes. Elements of the returned ExpressionSet or AffyBatch object are means over each probeset.

Author(s)

John Tillinghast

See Also

tranestAffyProbeLevel, sample.ind

Examples

library(LMGene)
library(Biobase)

data(sample.eS)
data(sample.ind)

# glog transform data
trs.eS <- transeS (sample.eS, 667, 65) 

# lowess normalize
ntrs.eS <- lnormeS(trs.eS) 

# take means over probesets
genesample.eS<- psmeans (ntrs.eS, sample.ind)

LMGene documentation built on April 28, 2020, 8:01 p.m.