Hi Simon, See below. If I'm not mistaken the padjGLM file has the adjusted pvals in the order that is in fit1, so I've been manually combining them. Let me know though if this is not the correct assumption.. Ingrid counts <- read.table ("pathtofile", header=TRUE, row.names=1) icv_c_ctrl_Design<- data.frame(row.names=colnames(counts), condition= c("c", "c", "c", "c", "c", "ctrl", "ctrl", "ctrl", "ctrl"), libType= c("DSN-SS", "DSN-SS", "DSN", "DSN-SS", "DSN", "DSN", "DSN-SS", "DSN", "DSN-SS")) library(DESeq) cdsFull <- newCountDataSet (counts, icv_c_ctrl_Design) cdsFull <-estimateSizeFactors(cdsFull) cdsFull <-estimateDispersions(cdsFull) fit1 <-fitNbinomGLMs(cdsFull, count ~ libType + condition) fit0 <-fitNbinomGLMs(cdsFull, count ~ libType) pvalsGLM <-nbinomGLMTest(fit1, fit0) padjGLM <-p.adjust(pvalsGLM, method = "BH") write.table(fit1, file="fit_c_ctrl") write.table(padjGLM, file="padjGLM_c_ctrl") On 3/21/2012 9:03 AM, Simon Anders wrote: > Dear Ingrid > > On 03/21/2012 03:18 PM, Ingrid Lindquist wrote: >> I am working with a multi-factor experimental design within DESeq and am >> confused as to how to (when to) export my results. I am wondering at >> what point can i write.table of my results to include both foldchange >> and padj values for each gene. > > Please post your workflow with the commands you use so that I can > indicate where the results become available. > > Simon > > _______________________________________________ > 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 -- Ingrid Lindquist National Center for Genome Resources 2935 Rodeo Park Drive East Santa Fe, NM 87505 (505) 995-4426 iel at ncgr.org