different fpkm values for one sample in cuffdiff isoform_exp.diff output

[liuxq]

i have three samples R1, R2 and R3, and i use cuffdiff to do differential expression analysis.

for a specific gene, its fpkm value for one sample has two value records, because each sample will be compare to other two samples respectively.


i find that in the isoform_exp.diff file, for one specific gene uc009ywh.3, the two fpkm values are inconsistent for one sample R2. when compared with R1 the fpkm value for uc009ywh.3 is 0, however, when compared with R3, the fpkm value is 21.6051.

how to explain the inconsistency?

[rboettcher]

Could you state which version of cufflinks etc. you are using and how your command looks like?

[liuxq]

Could you state which version of cufflinks etc. you are using and how your command looks like?

version of cufflinks is 2.0.2
the command is as follows
cuffdiff -o diff_out.ucsc -b hg19.fa -L R1,R2,R3 -u ./UCSC.hg19.gtf R1.bam R2.bam R3.bam

actually speaking, i have traced cufflinks for several versions. the problem exists all along