Question

Is the colnames of model.matrix on the page 34 in edgeR User's Guide?

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2002ymx02 • 0

@2002ymx02-21132

Last seen 4.6 years ago

Germany, Dresden, TUD

Hi Gordon Smyth and other authors of edgeR, It seemed that the colnames of design2 on page 34 in edgeR User's Guide were wrong. They should be (intercept), groupA and groupB, not (intercept), groupB and groupC, because groupC was releveled as reference. Could you check this?

Best, Mingxing Yang

edger • 743 views

ADD COMMENT • link updated 4.7 years ago by Gordon Smyth 50k • written 4.7 years ago by 2002ymx02 • 0

score 0 · Answer 1 · 2019-08-13

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Gordon Smyth 50k

@gordon-smyth

Last seen 5 hours ago

WEHI, Melbourne, Australia

Yes, you are right. Thanks for alerting us. Now fixed.

ADD COMMENT • link 4.7 years ago Gordon Smyth 50k

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Thank you for your edgeR and imma. Here is another typo: it shoud be CvsA=C-A, not CvsA=A-C in the last second line on page 31. And it could be better to say: .....genes that are always "significant" in red cells, not always "higher" in last line 6 on page 32, because for DE analysis, the first result we could see is whether genes are significant.

Best wishes, Mingxing Yang

ADD REPLY • link 4.7 years ago 2002ymx02 • 0

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it should be CvsA=C-A

OK.

And it could be better to say: .....genes that are always "significant" in red cells, not always "higher" in last line 6 on page 32,