Dear team,<br><br>I&#39;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 &#39;not significant&#39;.<br>
<br>My questions will be:<br><br>1. Since they are &#39;not signaficant&#39;, should I not take those genes into consideration even if they have high fold change?<br>2. Some of them have really low value_1 or value_2 (less than 1). Is this why they have a high q-value? <br>
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?<br><br>The reason I ask those questions is in my cuffdiff results, I found some really interesting genes of high fold change but they are &#39;not significant&#39; . I am really not sure whether I have to give they up because of the high q-value.<br>
<br>Thank you very much,<br><br>Qian<br clear="all"><br>-- <br>Qian Dong<br>Bauer Lab, MCBD<br>Simon Hall: 313-317<br>212 S. Hawthorne Dr.<br>Bloomington, IN 47405<br><a href="mailto:Email%3Adong3@indiana.edu">Email:dong3@indiana.edu</a><br>
Lab Phone:812-855-8443<br><br>