A Question About Comparing Two Samples In Cufflinks

Question

[camelbbs]

test_id    gene_id    gene    locus    sample_1    sample_2    status    value_1    value_2    log2(fold_change)    test_stat    p_value    q_value    significant
A1BG,NM_130786    A1BG,NM_130786    -    chr19:58858171-58874120    q1    q2    OK    0.0880865    46.1607    9.03353    -4.18911    2.80E-05    0.00093625    yes
A1BG-AS1,NR_015380    A1BG-AS1,NR_015380    -    chr19:58858171-58874120    q1    q2    OK    2.71793    2.21958    -0.292218    0.173229    0.862471    0.948357    no

Hi, I am curious how cuffdiff give the p_value and q_value while I compare just two samples. This is the result of gene_exp.diff. As I know, pvalue and qvalue can only given while comparing more than two samples in two groups.

Very appriecate if anybody can clear this.

Che

[camelbbs]

I see cuffdiff calculate the pvalue like this: http://cufflinks.cbcb.umd.edu/howitworks.html#hdif

It is so complicated, anyone can simple explain it. Thanks a lot!

Answer 1

[med.rdgmc]

It depends up on replicates, so just say, it will be 1 for both if no relicates are thre.