I have rnaseq data which I analyzed using the latest versions of tophat-cufflinks-cuffdiff ( that includes the new dispersion methods)
The authors mention that, "Because the test is now based on explicit sampling from the beta negative binomial, users will not see values less than 10^-5 by default" .
I understand this is the lowest possible p one will see, which then in turn outputs a uniform adj -p (0.00801514) for 45 of my genes that had equal or smaller than 10^ -5 p-val.
Is it legitimate to see the same p val for 100's of genes when it is NOT equal or less than 10^-5?
Thanks
The authors mention that, "Because the test is now based on explicit sampling from the beta negative binomial, users will not see values less than 10^-5 by default" .
I understand this is the lowest possible p one will see, which then in turn outputs a uniform adj -p (0.00801514) for 45 of my genes that had equal or smaller than 10^ -5 p-val.
Is it legitimate to see the same p val for 100's of genes when it is NOT equal or less than 10^-5?
Thanks
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