Hi,
I am using RNA-seq data. I have 3 time points in my data 6 months (young), 12 months (middle) and 28 months (old). I want to do a differential expression analysis across the 3 time points. I have used cuffdiff to do this:
cuffdiff -o /time -L young,middle,old -b /RGSC3.4.61.dna.toplevel.2.fa -u -N -T --library-type fr-secondstrand /allrat.combined.gtf /1.sam,/2.sam,/3.sam
/4.sam,/5.sam,/6.sam /7.sam,/8.sam,/9.sam
The output I get is a comparisons between "young and middle" and "middle and old". Does this seem correct? I would have expected a comparison of "young and old" whilst taking into account the differences in middle?
Thanks
I am using RNA-seq data. I have 3 time points in my data 6 months (young), 12 months (middle) and 28 months (old). I want to do a differential expression analysis across the 3 time points. I have used cuffdiff to do this:
cuffdiff -o /time -L young,middle,old -b /RGSC3.4.61.dna.toplevel.2.fa -u -N -T --library-type fr-secondstrand /allrat.combined.gtf /1.sam,/2.sam,/3.sam
/4.sam,/5.sam,/6.sam /7.sam,/8.sam,/9.sam
The output I get is a comparisons between "young and middle" and "middle and old". Does this seem correct? I would have expected a comparison of "young and old" whilst taking into account the differences in middle?
Thanks
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