Question

How to retrieve all logFCs fom "glmQLFTest()" output-edgeR?

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zhang.jianhai ▴ 10

@zhangjianhai-12955

Last seen 4.3 years ago

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

edgeR "glmQLFTest()" • 879 views

ADD COMMENT • link 6.9 years ago zhang.jianhai ▴ 10

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Dear Gordon Smyth,

Thank you very much.

I have resolved the problem using the latest versions.

Regards,

Jianhai

ADD REPLY • link 6.9 years ago zhang.jianhai ▴ 10

score 1 · Answer 1 · 2017-05-21

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Entering edit mode

Gordon Smyth 50k

@gordon-smyth

Last seen 4 hours ago

WEHI, Melbourne, Australia

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.

ADD COMMENT • link 6.9 years ago Gordon Smyth 50k