Hi all,

I am new to this list and have a question (below) related to -
selecting/filtering probesets from exprSet object prior to diff. exp. anal.

I'm also new to Bioconductor and am currently learning preprocessing of
microarray data (i.e. raw CEL files from the Affymetrix UG-133A array) and
then working
with the normlized exprSet object to detect differential gene expression of
tumor
(ovarian) samples compared with normal samples.  I am currently working
with a set
of ~33 tumor samples and ~7 normal samples.

Because my machine is 32 bit and cannot handle that much memmory
allocation,
for the preprocessing I am using a program called RMAExpress to produce the
normalized exprSet object.  With the exprSet object (I am calling "eset") I
am then using
Bioconductor for the differential gene expression analysis.

To start I have been creating a desgin matrix (as below)
(which I name "design") for linear modeling steps I am using
that come with the limma package.

 Normal Tumor
T1   0  1
T2   0  1
T3   0  1
T5   0  1
T7   0  1
N1  1  0
T8   0  1
T9   0  1
T10 0  1
T11 0  1
N2  1  0
T12 0  1
T13 0  1
T14 0  1
T15 0  1
N3  1  0



and then I am using the following code to produce a linear model, a
contrast matrix,
and a list of differentially expressed genes.


fit <- lmFit(eset, design)
cont.matrix <- makeContrasts(NormalvsTumor=Tumor-Normal, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)
fit2 <- eBayes(fit2)
topTable(fit2, number=100, adjust="BH") # use BH method

My question is this,
Is there a way to select or exclude ceratin probesets that I want or don't
want to be included in the
linear model before I produce the list (topTable) of differentially
expressed genes?

I have looked at the genefilter function but have not found specific
examples of how to do what I want.


Thanks in advance,
-M




-- 
Mark Baumeister

http://sites.google.com/site/lfmmab/

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