[BioC] Why the resuts are so different between the classic and the glm methods?

Gordon K Smyth smyth at wehi.EDU.AU
Fri Dec 13 06:01:31 CET 2013

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

--------- 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 
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.

-------------- 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

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