Hi, I hope that someone can be so gentle to help me. I'm analizing some data from RNA-Seq with TopHat and Cufflinks and I focus my attention on differently spliced genes. In particular, now I'm working on "maybe false positive", for example:
NM_001130171 Zfp207 Zfp207 chr11:80196780-80219375 day0 day3 OK 0.0000000 36.6325000 1.79769e+308 1.79769e+308 2.67658e-19 1.72370e-18 yes
this row comes from isoform_exp.diff file and the log2fold change is totally crazy because one sample is zero. So, I control the expression with expressionBarplot from cummeRbund, and the fpkm value of sample one was not zero! This function takes the information from another file, gene_exp.diff:
Zfp207 chr11:80196780-80219375 day0 day3 OK 26.4421 97.6658 1.88502 -15.6715 0 0 yes
The two files should be have the same results, but they are different and a p-value=0 is really strange.
Have someone some information about this? There is some normalization not explained in Cufflinks web site? What is the final true fpkm value?