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Old 05-11-2011, 02:24 AM   #1
Location: Israel

Join Date: Oct 2010
Posts: 37
Default Cufflinks differential expression problem

Hi all,

When running CuffDiff I got the following results for 3 samples:
Sample 1 FPKM - 47.01
Sample 2 FPKM - 0
Sample 3 FPKM - 0

And for the differential test:
ln(FC) test p-value significance
Sample1 vs. Sample 2 -1.79769e+308 NOTEST 0 no
Sample1 vs. Sample 3 -1.79769e+308 OK 0 yes

If both Sample2 and Sample 3 have an FPKM value of 0 why is there a difference in the differential expression?
Why wasn't a test conducted for the first pair? If there were enough fragments to conduct the test for the second pair, there should be enough for the first...

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Old 05-11-2011, 12:06 PM   #2
Cole Trapnell
Senior Member
Location: Boston, MA

Join Date: Nov 2008
Posts: 212

Can you send the mapped reads for this locus in each sample as a test example to our support mailing address? It's hard to say what's going on here just from these results.
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Old 05-12-2011, 12:08 AM   #3
Location: Israel

Join Date: Oct 2010
Posts: 37

Thanks for your reply Cole!
I sent you the reads to the help address just now.

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