Thread: DESeq2 error
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Old 09-07-2014, 09:54 AM   #6
Location: US

Join Date: Aug 2014
Posts: 23

Hi Devon, so what I am trying to do is to use DESeq2 to compare two data manipulation methods. The same RNAseq fastq dataset was used in tophat. Condition1 used coverage search (which takes a lot longer to run) while Condition2 used no coverage search. I suspect the additional coverage based junction search will not significantly impact reads and thus DE results. Although I still want to check.

Perhaps the reason why DESeq is having so much trouble with this comparison is because the counts are mostly identical between the two conditions?

To Michael, the mean fit worked and I will delve more into the manual to see why. However, the log2foldchange column doesn't make sense. The value is way too small for almost all of the genes with some being 0!


Last edited by stormin; 09-07-2014 at 10:00 AM.
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