Dear Nicolas, I noticed that my read counts are varying when I count the exact same sample twice. Specifically, genes that have counted reads in the first run are not represented at all (0 counts) in the second run, while others have exactly the same counts! I attached a shortened list of what my count tables look like in a tsv file, please note that I recounted the samples with the same options and annotation was provided via biomaRt. To explain the attached .tsv-file, I recounted the samples in order to make a comparison of Group1 vs Group1 treated and Group1 vs Group2 using separate objects. You can easily see the differences in reads counts in the first sample of both comparisons (Group1_1412.bam). Here's how I used the easyRNASeq function: DGElist = easyRNASeq(organism="Hsapiens", annotationMethod="biomaRt", gapped=TRUE, count="genes", summarization="geneModels", filesDirectory=getwd(), filenames=bamfiles, recursive=T, normalize=F, outputFormat="edgeR", conditions=conditions) I hope this problem can be solved easily, because I already handed the list of differentially expressed genes over to a colleague of mine who wants to validate these genes now. Best regards, Ren?