To whom it may concern,

I have questions about the output of "glmQLFTest()".

In my contrast matrix con.ma), there are 630 coefs, i.e. number of columns is 630, but when I run the following code, only 40 logFCs are shown: res <- glmQLFTest(fit, contrast=con.ma), topTags(res). 

In my research, I need to get "all the logFCs of the 630 contrasts". How can I retrieve them?

Thanks in advance.

Regards,

Jianhai

You're apparently using a version of edgeR and Bioconductor that is not the latest. Try running R 3.4.0 and installing the latest version of  edgeR.