Dear all,

In the Methods section, in the subsection, Testing for differential expression, it is mentioned that a gene is considered differentially expressped if FDR adjusted p-value is < 0.01 and estimated fold-change is greater than 1.5 (on a log2 scale).

For the estimated fold change, does the paper mean that avglogFC > 1.5 or FC > 1.5 and avglogFC > 0.58 (knowing that log2(1.5) = 0.58)?

Also, it is not clear to me how the p-value was calculated?

Thank you Ahmed

Hi Ahmed,

The code to reproduce the Genome Biology paper is located here, you will have to be running an older version of R and MAST in order for it to run without modification. Looking through the code, it seems we required a log fold change of log2(1.5) = .58. The P value was the "Hurdle" component using a likelihood ratio test.