[BioC] how to save the expression values for two color data after normalization
m.cowley at garvan.org.au
Tue Sep 28 01:23:43 CEST 2010
dat2$genes is probably a data.frame or matrix, not a vector
On 28/09/2010, at 12:03 AM, Steve Lianoglou wrote:
> On Mon, Sep 27, 2010 at 7:09 AM, Budhayash Gautam
> <budhayashgautam at gmail.com> wrote:
>> Dear all
>> i am working on some smd data which is basically two color data. i
>> have normalize the data by the following command
>>> dat2<-normalizeWithinArrays(dat, method="loess","normexp", offset=50)
>> but as now i am trying to save its expression values by the following
>> command its is not giving any genes names with respect to rows without
>> which further analysis (annotation etc ) could not be done .
>>> write.table(dat.m, "tgondiiexpressionvalues.txt", sep="\t", row.names=T, col.names=T, quote=F)
> This gives you probe id's, right? You can "reverse engineer" which
> probes map to which genes using several methods. Depending on the
> array you are using, one way would be to query biomart (using the
> biomaRt bioc package) for a list of probe id's for your chip and have
> it return the probe id & the gene symbol, or entrez id, or whatever
> you like.
> Another way would be to use one of the many annotation packages
> available from bioconductor.
>>> rownames(dat.m) <-dat2$genes
>> following error is coming .....
>> Error in dimnames(x) <- dn :
>> length of 'dimnames'  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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