Sean Davis scripsit 08/18/2011 03:38 PM: > On Thu, Aug 18, 2011 at 9:23 AM, geng chen<chengeng66666 at="" gmail.com=""> wrote: >> Dear Sir/Madam, >> >> I have read the paper of DESeq, it seems mainly be used for detecting >> differential expression genes. Could I use the same methods as genes to >> calculate the differential expression of isoforms? Thank you very much. > > You could check out the DEXSeq package, also. > > Sean Dear Geng Chen Yes. Note that DEXSeq 1. finds those genes in which isoforms are differentially expressed 2. within those genes, tries to determine which exons are affected in particular. This works well for genes with many exons, where the differential expression only affects a few exons. DEXSeq does not attempt to solve the isoform deconvolution problem. Best wishes Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber