ib,

Look at the status column. I suspect that for this example you given the status is HiData. Cuffdiff considers the expression are very high and no statistic testing would have been done for the gene. fpkm 2=0 could be misleading, as it may not be actually 0. I have encountered in a data set where several genes are expected to be highly expressed in all samples, but one of the fpkm values were all given as 0. Hope this helps.


Haiping

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On 10/15/2012 5:36 PM, i b wrote:
Dear forum,
whoever knows this please tell me!!!!!

Given two fpkm  . e.g. fpkm 1=2922828 and fpkm 2=0, why cuffdiff does
not calculate differential expression. those genes are listed in
cuffdiff as not significant and the log2 fold change is infinite ,
either negative or positve...how do i consider them when i want to
pull out the genes that are differentially expressed between treated
and untreated samples?

how do i interpret these data?

thanks,
ib
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