[BioC] se.exprs.pdf

[Mary Putt]

Hi,
I have a question about the output of se.exprs. I normalized a data set
using expresso and the model from Irizarry et al (2003) Biostatistics
paper.

rma.dta<-expresso(raw.data, normalize.method="quantiles.robust",
bkground.correct="rma", summary.method="medianpolish",
pmcorrect.method="pmonly")

I can extract the expression values using

exprs.rma<-exprs(rma.dta)
 and  could compute a sample standard deviation from

se.rma<-sqrt(apply(exprs.rma, 1, var)). The square of this estimates the

variance of the individual expression values.

I can also extract the model-based estimate of the standard deviation
from

se.model.rma<-se.exprs(rma.dta)

I'm not sure whether se.model.rma (squared) estimates the variance of
the individual espression values. For further clarification and
statistical notation pls see the attached pdf file.

This question was motivated by my observation that the sample standard
deviation is substantially larger than the model-based standard
deviation in a dataset that I am working with.

Many thanks in advance, Mary Puttse.

exprs.pdf
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