[BioC] how to save the expression values for two color data after normalization

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Sep 27 16:03:24 CEST 2010


On Mon, Sep 27, 2010 at 7:09 AM, Budhayash Gautam
<budhayashgautam at gmail.com> wrote:
> Dear all
> i am working on some smd data which is basically two color data. i
> have normalize the data by the following command
>> dat2<-normalizeWithinArrays(dat, method="loess","normexp", offset=50)
> but as now i am trying to save its expression values by the following
> command its is not giving any genes names with respect to rows without
> which further analysis (annotation etc ) could not be done .
>> dat.m<-dat2$M
>> rownames(dat.m)<-dat2$genes$ProbeName
>> write.table(dat.m, "tgondiiexpressionvalues.txt", sep="\t", row.names=T, col.names=T, quote=F)

This gives you probe id's, right? You can "reverse engineer" which
probes map to which genes using several methods. Depending on the
array you are using, one way would be to query biomart (using the
biomaRt bioc package) for a list of probe id's for your chip and have
it return the probe id & the gene symbol, or entrez id, or whatever
you like.

Another way would be to use one of the many annotation packages
available from bioconductor.

>> rownames(dat.m) <-dat2$genes
> following error is coming .....
> Error in dimnames(x) <- dn :
>  length of 'dimnames' [1] not equal to array extent

That's because the number of rows in your `dat.m` matrix does not
equal the length of your dat2$genes vector, so R can't make much sense
of the assignment you are trying to make.

Look at the result of:

R> nrow(dat.m) == length(dat2$genes)

Where did you get the dat2$genes vector? Perhaps you can show us what
you get from:

R> head(dat2$genes)

is it possible that the probe id's are the names() of this vector?
That could make your life a bit easier.

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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