[BioC] Calculate the relation between mRNA and miRNA

[Gordon K Smyth]

Dear Jack,

lmFit() allows NA values in the expression values but not in the design 
matrix.  If you must put NA values in a column of the design, then 
you need to remove them like this:

   anyna <- apply(is.na(miRNA),1,any)
   fit <- lmFit(mRNA[,!anyna], miRNA[!anyna,])

This code identifies rows of the design matrix containing NAs, then 
removes those samples from the data.

lmFit does not do this automatically, because I feel that this is 
something that a user should make a decision about deliberately.

Best wishes
Gordon

> Date: Fri, 22 Jun 2012 09:59:28 -0400
> From: Yao Chen <chenyao.bioinfor at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] [Limma] Calculate the relation between mRNA and miRNA
>
> Hi all,
>
> I have a problem to use lmFit calculated the correlation between mRNA and
> miRNA, because my miRNA data contained "NA" values.
>
> So if I use :lmFit(mRNA,miRNA), I got the message "Error in qr.default(x) :
> NA/NaN/Inf in foreign function call (arg 1)".
>
> The original "lm" function allow to included "NA", why lmFit can't?
>
> Thanks,
>
> Jack

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