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Old 09-06-2012, 06:32 AM   #1
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Location: Miami

Join Date: Feb 2009
Posts: 8
Default Cuffdiff-confidence interval

Hi, everybody, I have a problem about cuffdiff. I used cuffdiff to test differential expression. However, I checked the "genes.fpkm_tracking". All the FPKM estimate have q1_conf_lo=0, and q1_conf_hi a big number, which means the 95% confidence interval are very large. It seems not reasonable. I am not sure if the test statistic is calculated by this intervals. If it is, then the number of the deferentially expressed genes would be smaller.

I also try to use cufflinks to estimate the expression level. and "genes.fpkm_tracking" produced by cufflinks have reasonable intervals. I remember cuffdiff used cufflinks quantification engine. So they should have similar result, right? Anyone have any ideas for this problems?

Thanks a lot
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