[Bioc-sig-seq] RNAseq stat analysis
Simon Anders
anders at ebi.ac.uk
Mon Jul 6 21:30:06 CEST 2009
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
+---
| Dr. Simon Anders, Dipl. Phys.
| European Bioinformatics Institute (EMBL-EBI)
| Hinxton, Cambridgeshire, UK
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