Dear Bioconductor team, I am using DESeq and edgeR for analysis of count data and find differentially expressed genes and btw it worked very well. As input data I created read count. For that I used also Illumina's CASAVA and GenomeStudio. Unfortunately, Illumia changed the counting procedure. As of version 1.8 read counting is not possible anymore, they changed finally to base counting. Means all mappable bases which fulfil a given quality score will be counted. So by using high quality 50bp reads for mapping the counts will be around 50x higher compared to the read count method. By using the base counts in edgeR the number of differentially expressed genes is dramatically reduced. We normally compare DESeq and edgeR results and they fit around 80%. Using the base counts the results do not fit anymore. I divided all base counts by 50 to approximate the read count and the results look better, but not as good as before. Furthermore, I get uncertainties because of counting in splice site is more sophisticated. Nevertheless, my question is whether I can run edgeR using base counts and getting good results? Thanks, Marco -- Marco Groth