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

Thank you very much,


Qian Dong
Bauer Lab, MCBD
Simon Hall: 313-317
212 S. Hawthorne Dr.
Bloomington, IN 47405
Lab Phone:812-855-8443
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