about model.matrix in limma or edgeR
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Bogdan ▴ 670
@bogdan-2367
Last seen 5 months ago
Palo Alto, CA, USA

Dear all,

please if I may ask a question that may have been asked before, it is  about basics of limma and edgeR :

sometimes in the documentation and in some examples, the design matrix is specified as :

1) design <- model.matrix(~group)

and, in some other examples, as :

2) design <- model.matrix(~0+group, data=y$samples)

please could you let me know your recommendations of design1 vs design2. Thank you ;) !

 

bogdan

limma edgeR • 847 views
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@gordon-smyth
Last seen 9 hours ago
WEHI, Melbourne, Australia

Have you looked at Section 9.2 of the limma User's Guide? That explains the difference between these two design matrices in some detail. The section begins:

There are two different ways to form the design matrix. We can either

  1. create a design matrix which includes a coefficient for the mutant vs wild type difference, or
  2. create a design matrix which includes separate coefficients for wild type and mutant mice and then extract the difference as a contrast.
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Thank you Gordon for the quick reply. I am reading again the documentation now, and will let you know if i have any other questions ;)

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