Hi Bogdan,, As specified in the vignette, you should use raw tag counts and never RPKM. DESeq will perform the library size adjustment.
Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme High Throughput Functional Genomics Center European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delho...@embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On 26 Jul 2011, at 22:16, Bogdan Tanasa wrote: > Dear all, > > regarding DESeq package: would it be more appropriate to use raw tag counts > or RPKM values ? thanks, > > bogdan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > Bioc-sig-sequencing@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
