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Old 11-02-2011, 11:33 PM   #1
zeam
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Location: USA

Join Date: Oct 2010
Posts: 38
Default Cuffdiff:bug or misunderstanding

Hi there,
Recently, I'm using tophat and cufflinks to processing RNA -seq data.When I checked the cuffdiff results, I saw that if PRKM one of the sample was 0 then, then value of significant would be no.Take one gene for example,the gene below are significantly expressed in the two samples , but the p-value and the q-value are both not significant.Why was that happened? This is confusing me. My goal was to find differencially expressed genes , but how to choose a standard ?
###############################################
XLOC_000278 XLOC_000278 GRMZM5G842168 chr0:3478602-3478782 q2 q3 OK 0 942.574 1.79769e+308 1.79769e+308 0.129087 0.611177 no
###############################################
XLOC_000926 XLOC_000926 GRMZM2G046086 chr1:14288358-14288941 q2 q3 OK 0 34.8376 1.79769e+308 1.79769e+308 0.108366 0.595925 no
###############################################
Thanks,
Xie

Last edited by zeam; 11-02-2011 at 11:43 PM. Reason: Add more infor
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