Hello everyone,
I have been using cufflinks to get fpkm values and then analyzing these using the JMP statistical package for identifying between-group differential expression (8 cases and 8 controls). Can someone tell me if there is a way to do this using cuffdiff as well? From my reading of the manual, it seems that giving cuffdiff more than 2 sam files causes it to treat the data as a time series, which is not the case for my experiment. I considered just merging all the sam files from the 8 subjects in each group, but that way I will lose the power of the multiple replicates.
Any suggestions will be much appreciated,
Thanks,
Shurjo
I have been using cufflinks to get fpkm values and then analyzing these using the JMP statistical package for identifying between-group differential expression (8 cases and 8 controls). Can someone tell me if there is a way to do this using cuffdiff as well? From my reading of the manual, it seems that giving cuffdiff more than 2 sam files causes it to treat the data as a time series, which is not the case for my experiment. I considered just merging all the sam files from the 8 subjects in each group, but that way I will lose the power of the multiple replicates.
Any suggestions will be much appreciated,
Thanks,
Shurjo
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