[BioC] limma design matrix with common reference

Gordon K Smyth smyth at wehi.EDU.AU
Tue Nov 16 20:11:38 CET 2004

> Date: Tue, 16 Nov 2004 11:16:15 +0200
> From: "Ron Ophir" <ron.ophir at weizmann.ac.il>
> Subject: [BioC] limma design matrix with common reference
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <s199e19e.016 at wisemail.weizmann.ac.il>
> Content-Type: text/plain; charset=US-ASCII
>>From limma userguide chapter 9.3 Common Reference Designs it is
> suggested to fit the coefficients on RGList object:
> fit <- lmFit(RG, design)
> when I tried this I got an error message
> Error in array(x, c(length(x), 1), if (!is.null(names(x)))
> list(names(x),  :
>         dim<- : dims [product 362880] do not match the length of object
> [8]
> It seems to me that it is more reasonable to fit the coefficients on
> normalized dat and indeed when I trried to fit it on MAList object all
> went well.

Sorry, this is a typo in the User's Guide.  It doesn't make sense to fit a linear model to an
RGList object, and trying to do so will lead to the error above.  You are quite correct, the
linear model should be fit to the normalized MAList object.


> Ron

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