Dear team, I've been having some problem with cuffdiff results interpretation. I understand that on for a certain sample, it has to have a log2(fold change) that is larger than the cutoff and also have a q-value that smaller than a cutoff. I have a lot of genes that have a really high fold change and also high q-values so they are 'not significant'.
My questions will be: 1. Since they are 'not signaficant', should I not take those genes into consideration even if they have high fold change? 2. Some of them have really low value_1 or value_2 (less than 1). Is this why they have a high q-value? 3. How can I get a high q-value if both value_1 and value_2 are quite large and the fold change is also large? The reason I ask those questions is in my cuffdiff results, I found some really interesting genes of high fold change but they are 'not significant' . I am really not sure whether I have to give they up because of the high q-value. Thank you very much, Qian -- Qian Dong Bauer Lab, MCBD Simon Hall: 313-317 212 S. Hawthorne Dr. Bloomington, IN 47405 Email:do...@indiana.edu Lab Phone:812-855-8443
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