[BioC] Limma and EMPTY gene id for specific blocks of rows

Yannick Wurm Yannick.Wurm at unil.ch
Tue Mar 11 11:09:09 CET 2008

Hi Stanley,

you'll probably want to do something along these lines:
	>spotTypes <- readSpotTypes()

which requires that a SpotType.txt file in the current directory.  
Contents of the file look like this:
	SpotType	ID	Color
	Gene	*	black
	Spikein	alien*	red
	Blank	EMPTY	yellow

Then before fitting, you can do something like this:
	>isGene = MA.p$genes$Status=="Gene"
	>fit = lmFit(MA.p[isGene,], design)

Kind regards,

          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne

On Mar 11, 2008, at 8:43 , Ng Stanley wrote:

> Hi,
> I am using limma package to process some gpr files, which contained  
> gene id for specific blocks of rows. Couple of questions
> A) Before what stage should these "EMPTY" rows be deleted. I used  
> functions:
> backgroundCorrect, normalizeWithinArrays, lmFit, contrasts.fit,  
> eBayes ?
> B) In relation to A), are there any functions in limma that I can  
> invoke to
> delete those "EMPTY" rows ?
> C) What are those "EMPTY" rows ?
> Thanks
> 	[[alternative HTML version deleted]]
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