[Bioc-devel] Splitting design matrix contrast pivoting logic into a separate function?

Ryan C. Thompson rct at thompsonclan.org
Mon Sep 2 01:04:11 CEST 2013

Hi Gordon,

Thank you so much! That's exactly what I was looking for.


On Sun 01 Sep 2013 03:15:06 PM PDT, Gordon K Smyth wrote:
> Dear Ryan,
> See contrastAsCoef() in limma 3.17.23.
> Best wishes
> Gordon
> ---------------------------------------------
> Professor Gordon K Smyth,
> Bioinformatics Division,
> Walter and Eliza Hall Institute of Medical Research,
> 1G Royal Parade, Parkville, Vic 3052, Australia.
> http://www.statsci.org/smyth
> On Thu, 29 Aug 2013, Ryan C. Thompson wrote:
>> Hi Gordon,
>> I am currently working on some code that would benefit from having
>> direct access to the code in edgeR::glmLRT that handles
>> reparametrizing the design matrix so that the N linearly independent
>> components of the specified contrasts are represented in the first N
>> columns of the design matrix (i.e. the part of glmLRT that does all
>> the QR decomposition stuff). Would you consider splitting this logic
>> into a separate function that takes a design matrix and contrast
>> matrix and returns the equivalent reparametrized design matrix and
>> vector of coefficients?
>> Thanks,
>> -Ryan Thompson
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