[BioC] time course analyses Illumina RNA-seq data

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Mar 13 18:55:13 CET 2013

Hi Sandra,

On Wed, Mar 13, 2013 at 12:22 PM, Sandra Rehan <sandra.rehan at gmail.com> wrote:
> I am looking for software to analyze time course data for an Illumina
> gene expression data set (four lanes of paired end reads). I have two
> biological replicates for seven time points. All packages that I am
> aware of (bats, time course, edge) are designed for microarray data
> analysis. Does someone know of a software package designed for
> Illumina time course data?

There has been a recent thread on this list about doing a "proper"
timecourse analysis w/ limma using splines -- this thread resulted in
Gordon adding an additional section to the limma user's guide on how
to do so.

I wonder if you couldn't just use limma::voom to hammer your data into
a limma-workable-object and just do the timecourse analysis as
suggested w/ the microarray data?


Steve Lianoglou
Defender of The Thesis
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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