Hello, After performing a general Bioconductor update to the new version, I noticed that now the DEXseq package 1.8.0 is giving me different results from prrevious version 1.6.0. As a start, its function print dots "..." on the stdout which was not done in the previous version. This is not a big issue, the problem is that now I am obtaining different results. Generally, the padjust values are bigger. For example this exon: a1 a2 a3 b1 b2 b3 EXXXX 126 90 101 81 233 225 gets different results: geneID,exonID,dispersion,pvalue,padjust,meanBase,log2fold(b/a) old version: EXXXX,0.0684906370633231,0.00256847378387803,0.0321347815544768,129.94 1383199307,-0.217272839643456 new version: EXXXX,0.0928452378435829,0.00401881761350959,0.0587521235795571,129.94 1383199307,-0.213275654796358 as you can see the old one has a padjust below 0.05 and the other above 0.05, which is a big problem. I had a look in the NEWS section of the DEXSeq package, but i couldn't find any information about major changes. thank you very much, regards, [[alternative HTML version deleted]]

Dear Marco Marconi, I think that was the version where we changed from our original method, the one described on the paper to the recent apporach, you fill find this details in the section "Methodological changes since publication of the paper". As you might have noticed, the dispersions are very correlated as well as the p-values. I don't think the change in the p-value, and therefore the p-adjusted value, since it is not changing dramatically. The simplest thing would be to increase your FDR threshold a bit. Best regards, Alejandro > Hello, After performing a general Bioconductor update to the new version, I > noticed that now the DEXseq package 1.8.0 is giving me different results > from prrevious version 1.6.0. As a start, its function print dots "..." on > the stdout which was not done in the previous version. This is not a big > issue, the problem is that now I am obtaining different results. Generally, > the padjust values are bigger. > > For example this exon: > > a1 a2 a3 b1 b2 b3 > EXXXX 126 90 101 81 233 225 > > gets different results: > > geneID,exonID,dispersion,pvalue,padjust,meanBase,log2fold(b/a) > > old version: > EXXXX,0.0684906370633231,0.00256847378387803,0.0321347815544768,129. 941383199307,-0.217272839643456 > > new version: > EXXXX,0.0928452378435829,0.00401881761350959,0.0587521235795571,129. 941383199307,-0.213275654796358 > > > as you can see the old one has a padjust below 0.05 and the other above > 0.05, which is a big problem. > > > I had a look in the NEWS section of the DEXSeq package, but i couldn't find > any information about major changes. > > > thank you very much, 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