Hi James,

I used the following instructions in R (mydata <- ReadAffy(), mycomp <-
gcrma (mydata), write.table (mycomp, "mytext.txt", sep="\t")
or I called "mydata<-expresso(...,methods.summarization="median.polish',
....)".  In the results table, I obtained an expression value
per PROBE, and I would like to have an expression value per GENE. I know
that RMA/GCRMA could use median polish to summarize
the probes for a gene and to ask the question more specifically: is there
anything that the code I use  is missing ? In the final results
table, I would like to have the expression values for 10000-12000 genes
instead of having expression values for 22000 probes. Thanks,

Bogdan



# Read Affy CEL files
data <- ReadAffy()\
# Normalize and do summation using gcrma
eset <- gcrms (data)
#
# Noe eset contains all the information that you require
#
# to get a data frame of expression values, use exprs command
evals <- exprs (eset)
#
# The command below will tell you that it is a data frame
class (evals)
#
# You can write out tab separated expression values to be used by other
programs using the command
write.table (evals, "expressvals.txt", sep="\t")
#
#
Send me questions if you have any

On 9/6/07, James W. MacDonald <jmacdon@med.umich.edu> wrote:
>
> Hi Bogdan,
>
> Bogdan Tanasa wrote:
> > Hi all,
> >
> > I would like to ask for an information: I carry the array analysis for a
> > large dataset (40 samples * 2 replicates);
> > the arrays are Affy U133A, and I use GCRMA and invariant set
> normalization.
> > Please could you  let me know
> > the way I could do the probe summarization for these arrays. Thanks and
> best
>
> GCRMA _is_ a method to do probe summarization. Maybe you are asking a
> different question?
>
> Best,
>
> Jim
>
>
> > regards,
> >
> > Bogdan
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > Search the archives:
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>
>
> --
> James W. MacDonald
> University of Michigan
> Affymetrix and cDNA Microarray Core
> 1500 E Medical Center Drive
> Ann Arbor MI 48109
> 734-647-5623
>
>

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