CummeRbund plots

[godzilla07]

I have just loaded the latest CummeRbund program v2.01 and have a few questions. My RNAseq data is from 3 time points where each timepoint has a control C1, C2, C3 and an experimental condition E1 , E2 and E3. I have created cuffdiff output for all pairwise comparisons C1_E1, C2_E2, C3_E3. Should I save all cuffdiff output into a single directory for creating plots for all conditions? Also how do you save plots that are generated with CummeRbund?

[glados]

I have just loaded the latest CummeRbund program v2.01 and have a few questions. My RNAseq data is from 3 time points where each timepoint has a control C1, C2, C3 and an experimental condition E1 , E2 and E3. I have created cuffdiff output for all pairwise comparisons C1_E1, C2_E2, C3_E3. Should I save all cuffdiff output into a single directory for creating plots for all conditions? Also how do you save plots that are generated with CummeRbund?

Did you run cuffdiff 3 times for each paired comparison? Then you'll loose the biological replicate variance and have to rely on cuffdiff's guessed variance. But seeing as the samples are paired, I don't really know how you would do it otherwise. I'm actually wondering this since I have paired data but don't know how to keep the paired information when running cuffdiff. For example: Family1_sampleA, Family1_sampleB, Family2_sampleA, Family2_sampleB, etc.