Hello again, I'm writing this time to ask about setting up more complex formulae to test for significant interaction between independent variables in DEXSeq. Using the example from the manual, to test for an interaction between library type and condition, how would I set this up? The syntax here is a bit more involved than with DESeq, and I can't seem to find anything in the archives that answers my question... Thanks, Elena

Dear Elena, Thank you for your email. If I understood correctly, to test for an interaction between condition and type with the exons, it would be like this (example in the pasilla dataset): data("pasillaExons", package="pasilla") pasillaExons<- estimateSizeFactors( pasillaExons ) pasillaExons<- estimateDispersions( pasillaExons, count ~ sample + (condition * type) * exon ) formula0<- count ~ sample + exon + condition + type + condition:type formula1<- count ~ sample + exon + condition + type + (condition:type) * I(exon == exonID) pasillaExons<- testForDEU( pasillaExons, formula0=formula0, formula1=formula1 ) Best wishes, Alejandro Reyes > Hello again, > > I'm writing this time to ask about setting up more complex formulae to > test for significant interaction between independent variables in > DEXSeq. Using the example from the manual, to test for an interaction > between library type and condition, how would I set this up? The > syntax here is a bit more involved than with DESeq, and I can't seem > to find anything in the archives that answers my question... > > Thanks, > Elena > > _______________________________________________ > 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