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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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About obtaining DE genes #124

Closed ahmedabbas81 closed 4 years ago

ahmedabbas81 commented 4 years ago

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 avg_logFC > 1.5 or FC > 1.5 and avg_logFC > 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

ahmedabbas81 commented 4 years ago

Can you please answer?

amcdavid commented 4 years ago

"Issues" are for bug reports only. Please read the instructions on the README. Methods/applications questions are to be posted on support.bioconductor.org

ahmedabbas81 commented 4 years ago

Ok, thanks. I posted it on support.bioconductor.org