Question: Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
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gravatar for 2002ymx02
8 days ago by
2002ymx020
Germany, Dresden, TUD
2002ymx020 wrote:

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 • 57 views
ADD COMMENTlink modified 7 days ago by Gordon Smyth38k • written 8 days ago by 2002ymx020
Answer: Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
0
gravatar for Gordon Smyth
7 days ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

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

ADD COMMENTlink written 7 days ago by Gordon Smyth38k

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 REPLYlink modified 7 days ago • written 7 days ago by 2002ymx020
1

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,

No, the text is correct as it stands. The reference to "higher" is deliberate.

ADD REPLYlink modified 6 days ago • written 7 days ago by Gordon Smyth38k

Thank you Prof. Gordon for your reply.

ADD REPLYlink written 7 days ago by 2002ymx020
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