[Bioc-sig-seq] RNAseq stat analysis

[Simon Anders]

Hi Eric

Eric Bonnet wrote:
> We have mRNA expression data that was generated by solexa-illumina deep
> sequencing (75 nt reads), for two developmental stages, and we would
> like to have genes that are differentially expressed, by using
> procedures that were developed for microarrays, like samr, siggenes or
> limma.

The developers of limma have also published a package, called "edgeR",
that is meant to deal with count data as obtained by SAGE or RNA-Seq.

This might be a more proper solution than working with pseudo-counts.

http://www.bioconductor.org/packages/2.4/bioc/html/edgeR.html

The theory is described here: (I hope I got the right paper.)

Mark D. Robinson and Gordon K. Smyth:
Moderated statistical tests for assessing differences in tag abundance
Bioinformatics 23: 2881-2887.


Cheers
  Simon

	

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| Dr. Simon Anders, Dipl. Phys.
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