Hello all,
I run the Tuxedo pipeline to find differentially expressed genes btw 2 phenotypes (3 replicates for each) but in the end I get p-values limited to "0.00005" in CuffDiff output, nothing smaller; 1264 of 23779 genes (human) have that limitation so this is not their actual p-value, most of them should be much more significant. I have the latest version of CuffDiff (2.1.1). In the older versions I didn't have such a problem.
I don't know what I miss but I appreciate if you can help.
I run the Tuxedo pipeline to find differentially expressed genes btw 2 phenotypes (3 replicates for each) but in the end I get p-values limited to "0.00005" in CuffDiff output, nothing smaller; 1264 of 23779 genes (human) have that limitation so this is not their actual p-value, most of them should be much more significant. I have the latest version of CuffDiff (2.1.1). In the older versions I didn't have such a problem.
I don't know what I miss but I appreciate if you can help.
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