I have samples of 4 different conditions. Let's say untreated/treated and tissue A/tissue B.
#1: tissue A untreated
#2: tissue B untreated
#3: tissue A treated
#4: tissue B treated.
I need to compare between the treated vs untreated samples and also between samples.
What is the proper way to use cuffdiff to compare the samples?
Run cuffdiff with the pair of samples to compare or run it with all samples and use commeRbund to select the pairs I want to compare?
For example, if I want to compare condition #3 and #4, do I need to run cuffdiff with #3 and #4 or run it with all samples and select #3 and #4 using cummeRbund?
Thanks,
#1: tissue A untreated
#2: tissue B untreated
#3: tissue A treated
#4: tissue B treated.
I need to compare between the treated vs untreated samples and also between samples.
What is the proper way to use cuffdiff to compare the samples?
Run cuffdiff with the pair of samples to compare or run it with all samples and use commeRbund to select the pairs I want to compare?
For example, if I want to compare condition #3 and #4, do I need to run cuffdiff with #3 and #4 or run it with all samples and select #3 and #4 using cummeRbund?
Thanks,
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