Dear Vincenzo, Unfortunately I don't think I can answer that. Perhaps others on the List could help. BW, Natasha From: Vincenzo Capece [mailto:vivo0304@gmail.com] Sent: 01 October 2012 09:04 To: Natasha Sahgal Subject: Re: [BioC] DESeq - working with more than 2 conditions Thanks a lot Natasha, edgeR is exactly what I was looking for. I am also a statistics beginner and I have an another question ,but I don't know if it's correct or not: To compute BCV in edgeR, why the developers didn't use ANOVA? I think that the MDS in edgeR is the same of SSB(sum of squares between) in ANOVA. Right? Thank you very much. On 13 September 2012 10:46, Natasha Sahgal <nsahgal@well.ox.ac.uk<mailto:nsahgal@well.ox.ac.uk>> wrote: 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=""> [mailto:bioconductor- bounces@r-project.org<mailto:bioconductor-bounces@r-project.org>] On Behalf Of Vincenzo Capece Sent: 13 September 2012 07:53 To: bioconductor@r-project.org<mailto:bioconductor@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@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Regards, Capece Vincenzo [[alternative HTML version deleted]]

Thanks a lot Natasha, edgeR is exactly what I was looking for. I am also a statistics beginner and I have an another question ,but I don't know if it's correct or not: To compute BCV in edgeR, why the developers didn't use ANOVA? I think that the MDS in edgeR is s sort of SSB(sum of squares between) in ANOVA. Thank you very much. On 13 September 2012 10:46, Natasha Sahgal <nsahgal@well.ox.ac.uk> wrote: > 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@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@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Regards, Capece Vincenzo [[alternative HTML version deleted]]

Dear Vincenzo, You may also want to take a look at the baySeq package, which handles multiple conditions in a different fashion to the glm approach of edgeR and DESeq - in some scenarios this is a better way to think about the data, in others, not. Tom