Cufflinks FPKM and confidence intervals - how to tell if the gene is expressed or not

[sindrle]

Here are three examples:

One gene has a FPKM value, but the confidence interval (CI) is from zero.

The other gene does not have a FPKM value, but does have a CI including non-zero value.

The third has a CI not including the FPKM


ID FPKM CIlow CIhi

ENSMUSG00000022262 0,00350045 0 0,0128089

ENSMUSG00000089555 0 0 133,208

ENSMUSG00000092983 3869,89 0 10,2497


So, what can we say about these genes? Are they expressed or not?

[sindrle]

I guess another Cufflinks bug.... I choosed Cufflinks 2.1.1 due to Cuffdiff errors in 2.0.2, but here it seams Cufflinks 2.1.1 has a bug, even if Cuffdiff 2.1.1 works... :S

http://seqanswers.com/forums/showthread.php?t=39758