Hi Joel, The mailing list will not distribute large attachments, so we can't see your code script. Most likely you've made an error in the script, because the classic and glm pipelines in edgeR should give very similar results for a two group comparison. We would need to see the code to tell what the error is. We shouldn't need to see your data, just the code. Best wishes Gordon --------- original message ----------- Jiantao Yu joelyu.2003 at gmail.com Thu Dec 12 22:54:05 CET 2013 Dear Sir/Madam, When I used edgeR to do RNA-Seq analysis, I found the datasets of the resulting DEGs generated by 'Classic' and 'GLM' methods are very different, the former contain ~460 DEGs, whereas the latter generate ~27,000 DEGs. I don't know why this was happening. I attached the scripts and the source data I used, hope you would help me to explain this. Joel -------------- next part -------------- "mu1.bam" "mu2.bam" "mu3.bam" "wt1.bam" "wt2.bam" "wt3.bam" "AT1G01010" 50 89 54 69 71 56 "AT1G01020" 218 261 198 309 248 241 "AT1G01030" 27 47 26 50 48 23 "AT1G01040" 582 676 466 202 229 830 "AT1G01046" 10 11 8 6 6 5 ... ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}