Question: Cuffdiff Results Interpretation: High Fold Change But Not Significant
gravatar for Qian Dong
6.1 years ago by
Qian Dong50
Qian Dong50 wrote:
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 Lab Phone:812-855-8443
rna-seq cuffdiff • 2.2k views
ADD COMMENTlink modified 3.8 years ago by cmayer0 • written 6.1 years ago by Qian Dong50
gravatar for cmayer
3.8 years ago by
United States
cmayer0 wrote:

I have the same issue as well.  Can someone please enlighten me on the parameters that define a comparison with Significance: NO

ADD COMMENTlink written 3.8 years ago by cmayer0
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