I use edgeR for mRNA analysis and I want to see the difference in BCV between the control group and the treated group. I see that there is an argument called group in the estimateCommonDisp function, but I can not find examples on how to use it. It seems logic to use group=y$samples$group or something like that (where y is my DGElist object) but that does not work. Is there somewhere where I can read about this? I have searched a lot without success.
Thanks for your response! I thought that was possible since I saw a comparison between BCV in normal and tumor tissue. I also do not understand this: if I take all samples into consideration when calculating the BCV, wouldn't the value be very affected if there is a big expression difference between the controles and the treated ones? I mean, then the differences wouldn't be due to genetic biological variance, but rather to differences caused by the treatment. Perhaps a stupid thought...
And thanks for your advice regarding the workflow. I will definitely look at it!
Where did you see testing for differences in BCV between groups using edgeR?
BCV measures the variation between the biological replicates (i.e., samples within the groups). The group information is taken into account when estimating the BCV.