Hi Jenny,

I've had luck using a combination of the features presented in the packages
iRanges, genomeIntervals, BSgenome and edgeR (for statistics). Please feel
free to inquire if you like to discuss the details more.

Johannes Waage
University of Copenhagen

On Thu, May 28, 2009 at 9:45 PM, Jenny Drnevich <drnevich@illinois.edu>wrote:

> Hi,
>
> Anyone working with Illumina's Digital Gene Expression data? It's
> sequencing 17mer NLA3 "tags" pulled from 3' ends of transcripts on
> Illumina's GAII. I have the sequence data processed already and read counts,
> and now I'm just starting to try to estimate expression levels. I think I
> can do it all with tools already available in Bioconductor; I'm looking for
> someone who would be interested in having discussions on the best way to
> analyze this sort of data. I thought I'd try here first, and then the BioC
> mailing list.
>
> Thanks,
> Jenny
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich@illinois.edu
>
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>

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