cuffdiff2 fails to find diff expressed genes!!??

[colinmolter]

Hello,

I processed 8 breast cancer samples, 4ER+ and 4ER- using tophat2/cufflinks2/cuffmerge2/cuffdiff2/cummeRbund.

The expression of the gene GREB1 is nearly equal to 0 for the 4 ER-
and ~100 for ER+:

cuff <- readCufflinks()
expr=repFpkmMatrix(genes(cuff))
expr[rownames(expr)=='XLOC_011466',]
Neg_0 Neg_1 Neg_2 Neg_3 Pos_0 Pos_1 Pos_2 Pos_3
XLOC_011466 0.182529 0.791468 0.721075 0.15861 35.9609 231.247 64.1414 39.4893

However, the result of cuffdiff is:
diffData(getGene(cuff, 'GREB1'))
gene_id sample_1 sample_2 status value_1 value_2
log2_fold_change test_stat p_value q_value significant
1 XLOC_011466 Neg Pos OK 0.460534 92.726
7.65352 -1.1267 0.25987 0.999954 no

How can you explain this. It seems not consistent for me. I would have
expected a nice q value, a significant test, etc.

thanks for feedbacks,
colin

ps. data were downloaded from SRA/GEO : GSE27003 and are available at inSilico: https://insilico.ulb.ac.be/app/browse?q=GSE27003