Hello at all,

I use TopHat and Cufflinks to process some human RNA-seq data with an annotation gft-file for known genes (this means my pipeline is: TopHat -> Cuffdiff).

In the resulting gene_expr.diff file I obtain q-values greater than 1:

Since I thought that a q-value is a probability (fdr corrected p-value) it should not be greater than 1.

Its clear to me that when the p-value is corrected there can be q-values greater than 1 but I thought its limited to 1 in this cases. I am confused about the values, 1.08 is a very small value assuming the q-value is not a probability anymore (then I would expect higher values) but its to big for a rounding error I think.

Maybe I got there something wrong. Could someone explain it to me?

Thanks in advance,

Oliver

I use TopHat and Cufflinks to process some human RNA-seq data with an annotation gft-file for known genes (this means my pipeline is: TopHat -> Cuffdiff).

In the resulting gene_expr.diff file I obtain q-values greater than 1:

Code:

> range(expr$q_value) [1] 0.00000 1.08198

Its clear to me that when the p-value is corrected there can be q-values greater than 1 but I thought its limited to 1 in this cases. I am confused about the values, 1.08 is a very small value assuming the q-value is not a probability anymore (then I would expect higher values) but its to big for a rounding error I think.

Maybe I got there something wrong. Could someone explain it to me?

Thanks in advance,

Oliver

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