hello chintanu,
      You are very much right. Your query isn't related to use of
Bioconductor.
I'm not sure whether you are talking about cDNA microarray data or just cDNA
counts from a cDNA library. Nevertheless, those repeated gene-Ids (different
expression values) are due to alternative transcripts. Due to different exon
constitution and/ or different UTR lengths, alternative transcripts would
have variable stability and also functional repertoire.
 So it is for you to take the call as to whether average out the alternative
transcripts to make downstream analysis simpler or do a transcript-wise
analysis and take account of the actual variability in the cell.


regards,

amit mandal
Graduate student
Genomics & Molecular Medicine Lab
IGIB
Delhi

On Mon, Aug 31, 2009 at 11:23 AM, Chintanu <chintanu@gmail.com> wrote:

> Hi,
>
> I’m not sure whether it’s directly related to Bioconductor. Even if it’s
> not, I would appreciate if I could get some pointers.
>
> When I normalize a set of cDNA dataset (patients), I come up with several
> repeated gene-Ids that have different expression values. Wonder how to deal
> with (combine!) these cDNA gene-repeats such that ultimately one gene
> refers
> only to one expression-value per patient.
>
> Thank you.
>
> Kind regards,
>
> Chintanu
>
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>
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