Dear all, I am a R beginner and I hope you can help me. I have a question about DESeq: DESeq works fine if I have 2 conditions(treated,untreated) Example: treated untreated ENSMUSG00000000001 193 254 ENSMUSG00000000003 0 0 ENSMUSG00000000028 10 13 ENSMUSG00000000031 0 4 ENSMUSG00000000037 8 9 ENSMUSG00000000049 6 8 ... ... ... but if I have data about more than two conditions, for instance 1-month-treated,3-months-treatead, 6-months-treated,untreated, can I use DESeq? If not, Which R package (if it exists)do you suggest to use? Thanks in advance. Regards. [[alternative HTML version deleted]]

Dear Vincenzo, You could try to use the edgeR package (and the glm method within it). Also, if I am not mistaken, you could use DESeq but you have to use the glm method there. Hope that helps, Natasha -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Vincenzo Capece Sent: 13 September 2012 07:53 To: bioconductor at r-project.org Subject: [BioC] DESeq - working with more than 2 conditions Dear all, I am a R beginner and I hope you can help me. I have a question about DESeq: DESeq works fine if I have 2 conditions(treated,untreated) Example: treated untreated ENSMUSG00000000001 193 254 ENSMUSG00000000003 0 0 ENSMUSG00000000028 10 13 ENSMUSG00000000031 0 4 ENSMUSG00000000037 8 9 ENSMUSG00000000049 6 8 ... ... ... but if I have data about more than two conditions, for instance 1 -month-treated,3-months-treatead, 6-months-treated,untreated, can I use DESeq? If not, Which R package (if it exists)do you suggest to use? Thanks in advance. Regards. [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Dear Vincenzo > I have a question about DESeq: DESeq works fine if I have 2 > conditions(treated,untreated) > Example: > treated untreated > ENSMUSG00000000001 193 254 > ENSMUSG00000000003 0 0 Well, this is not a great example, as your conditions are not replicated, but, of course, that was not your question. > but if I have data about more than two conditions, for instance > 1-month-treated,3-months-treatead, 6-months-treated,untreated, can I use > DESeq? If not, Which R package (if it exists)do you suggest to use? Of course, there are plenty of methods to work with more than two conditions, by usign generalized linear models (GLMs). What you need to do depends on the question you want to ask. For two conditions, there is one obvious question, namely: Which genes are significantly stronger in condition A, and which ones are stronger in condition B? In your case, what would the question be? Simon

Dear Vincenzo please have a look at Section 4 of the DESeq vignette. Best wishes Wolfgang On 9/13/12 8:53 AM, Vincenzo Capece wrote: > Dear all, > I am a R beginner and I hope you can help me. > I have a question about DESeq: DESeq works fine if I have 2 > conditions(treated,untreated) > Example: > treated untreated > ENSMUSG00000000001 193 254 > ENSMUSG00000000003 0 0 > ENSMUSG00000000028 10 13 > ENSMUSG00000000031 0 4 > ENSMUSG00000000037 8 9 > ENSMUSG00000000049 6 8 > ... > ... > ... > > > but if I have data about more than two conditions, for instance > 1-month-treated,3-months-treatead, 6-months-treated,untreated, can I use > DESeq? If not, Which R package (if it exists)do you suggest to use? > > Thanks in advance. > Regards. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber