Cufflinks differential expression problem

[Rachelly]

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...

Thanks,
Rachelly.

[Cole Trapnell]

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.

[Rachelly]

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

Rachelly.