Hello, What R packages for differential expression analysis of mRNA-seq data are currently set up to do statistical testing with two main effects (two-way ANOVA)? I know that the latest versions of DESeq and edgeR can do this for genes; I know DEXSeq can do this for exons; I don't think that the latest versions of baySeq, DEGSeq or cuffdiff [the latter of which is not in R, obviously] can currently do this. Would anyone in-the-know care to update that? If there's a new software package that I missed, please let me know about that too. Thanks! Elena

Dear Elena, edgeR does DE analysis at the gene or exon level, indeed any level that counts are summarized at. Any package that fits genewise Poisson or negative binomial glms can claim to handle two-way anova, as well as more complex experiments. The situation as of a little less than a year ago was reviewed in our paper on this topic: http://nar.oxfordjournals.org/content/40/10/4288 There are a few more packages now, for example QuasiSeq on CRAN. Best wishes Gordon ------------ original message ------------- [BioC] RNA-seq analysis and two-way ANOVAs Elena Sorokin sorokin at wisc.edu Thu Aug 23 23:49:50 CEST 2012 Hello, What R packages for differential expression analysis of mRNA-seq data are currently set up to do statistical testing with two main effects (two-way ANOVA)? I know that the latest versions of DESeq and edgeR can do this for genes; I know DEXSeq can do this for exons; I don't think that the latest versions of baySeq, DEGSeq or cuffdiff [the latter of which is not in R, obviously] can currently do this. Would anyone in-the-know care to update that? If there's a new software package that I missed, please let me know about that too. Thanks! Elena ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}