I am quite new to RNA-seq analysis, but what I have learned so far is that replicates are important. If you have this result with no replicates then P-values are more or less meaningless. You can also gauge what is happening by looking at the modelled read count output. If the counts are both less than 50ish you are unlikely to have a robust result for that gene/transcript.
Ian
________________________________________ From: galaxy-user-bounces@lists.bx.psu.edu [galaxy-user-bounces@lists.bx.psu.edu] on behalf of Malik, Shivani [Shivani.Malik@ucsf.edu] Sent: 11 March 2014 21:43 To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] Cuffdiff output
Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. I have genes which show ~8 fold change between 2 conditions: eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is threshold of FPKM below which Cuffdiff does not consider it an FPKM to be valid and hence significance in "no"? What downstream analysis should I use to extract a meaningful list of genes from the Cuffdiff data?
Also, I filtered out FPKMs which were below 5 in both conditions? Is that reasonable?
Thanks Shivani
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