thanks, Wolfgang, I realize that. I did not have time yesterday but will do some more investigating myself today and if nothing shows up I will provide code etc.. Ina ----- Original Message ----- From: "Wolfgang Huber" <whuber@embl.de> To: "Ina Hoeschele" <inah at="" vbi.vt.edu=""> Cc: "bioconductor" <bioconductor at="" stat.math.ethz.ch="">, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> Sent: Friday, July 12, 2013 9:39:23 AM Subject: Re: [BioC] voom Dear Ina thanks. The problem report is a little unspecific? I presume that the people who could respond to this would need to know - the exact code you are running - version numbers (sessionInfo) - the plots that you are getting - (ideally and I am not sure it's needed although it doesn't harm) the offending data, in anonymised form. Best wishes Wolfgang On 11 Jul 2013, at 22:21, Ina Hoeschele <inah at="" vbi.vt.edu=""> wrote: > Hi, > I'm using limma's voom function on a (human) RNAseq dataset (regular transcript based count matrix). When I do an MDS plot on the input count matrix, all looks "normal". When I do the same plot on the output log CPM matrix (E), the samples (N=329) cluster strongly into two groups of about equal size. This happens no matter how I run voom (with or without design matrix, passing count matrix and adjusted lib sizes, or DGE obj). > Thanks, Ina > > _______________________________________________ > 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

thanks, Wolfgang, I realize that. I did not have time yesterday but will do some more investigating myself today and if nothing shows up I will provide code etc.. Ina ----- Original Message ----- From: "Wolfgang Huber" <whuber@embl.de> To: "Ina Hoeschele" <inah at="" vbi.vt.edu=""> Cc: "bioconductor" <bioconductor at="" stat.math.ethz.ch="">, "Bioconductor mailing list" <bioconductor at="" r-project.org=""> Sent: Friday, July 12, 2013 9:39:23 AM Subject: Re: [BioC] voom Dear Ina thanks. The problem report is a little unspecific? I presume that the people who could respond to this would need to know - the exact code you are running - version numbers (sessionInfo) - the plots that you are getting - (ideally and I am not sure it's needed although it doesn't harm) the offending data, in anonymised form. Best wishes Wolfgang On 11 Jul 2013, at 22:21, Ina Hoeschele <inah at="" vbi.vt.edu=""> wrote: > Hi, > I'm using limma's voom function on a (human) RNAseq dataset (regular transcript based count matrix). When I do an MDS plot on the input count matrix, all looks "normal". When I do the same plot on the output log CPM matrix (E), the samples (N=329) cluster strongly into two groups of about equal size. This happens no matter how I run voom (with or without design matrix, passing count matrix and adjusted lib sizes, or DGE obj). > Thanks, Ina > > _______________________________________________ > 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