Dear list members, I want to ask a question about DESeq or package with similar functionality. Can DESeq allow more than 2 samples to used for estimating differential expression? My aim was that If I have tissue A, B and C, and I want to find genes specifically high expressed in tissue A. Is there a way to do that by DESeq? or other packages? What if I have 4,5, or 10 tissues? Is it possible to do that? Thanks in advance for your response. Best wishes. Daofeng [[alternative HTML version deleted]]

Dear Daofeng searching for tissue-specific genes is a somewhat different question from looking for differential expression. Many other people may have many different suggestions (and could post them here), but a useful starting point for you could be this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154617/?tool=pubmed#SD1 A Gene Expression Barcode for Microarray Data by Michael Zilliox and Rafael Irizarry. In fact, this should be much easier with RNA-Seq data than for microarrays. For visualisation / data exploration / density estimation, DESeq's variance stabilising transformation could be useful. Best wishes Wolfgang Apr/9/12 8:19 PM, Daofeng Li scripsit:: > Dear list members, > > I want to ask a question about DESeq or package with similar functionality. > Can DESeq allow more than 2 samples to used for estimating differential > expression? > > My aim was that If I have tissue A, B and C, and I want to find genes > specifically high expressed in tissue A. Is there a way to do that by > DESeq? or other packages? > > What if I have 4,5, or 10 tissues? Is it possible to do that? > > Thanks in advance for your response. > > Best wishes. > Daofeng -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber