[BioC] se.exprs

[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. I have a pdf file that explains some
of the notation if this is helpful--but it is too long to be accepted by
standard bioconductor means--I can send to individuals if this is
helpful. 


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 Putt
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