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 | office phone +44-1223-492680, mobile phone +44-7505-841692 | preferred (permanent) e-mail: [email protected] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
