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-boun...@lists.bx.psu.edu 
[galaxy-user-boun...@lists.bx.psu.edu] on behalf of Malik, Shivani 
[shivani.ma...@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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