[BioC] MA plots without bg correction (mArray)

[Jean Yee Hwa Yang]

The quick way  to do MA-plots with no background subtraction is to remove
the background values from marrayRaw object

e.g.
maRb(christian.raw) <- maGb(christian.raw) <- matrix(0,0,0)
maPlot(christian.raw[,1])


Jean

On Mon, 8 Dec 2003, Foata,Francis,LAUSANNE,NRC/N&H wrote:

> Hello, I'm using the mArray package and I would like to make MA plots
> WITHOUT background correction. I tested the following R code :
> 
> xma<-log2(maRf(christian.raw[,1])/maGf(christian.raw[,1]))
> yma<-0.5*log2(maGf(christian.raw[,1])+maRf(christian.raw[,1]))
> maPlot (christian.raw[,1], x=yma, y=yma, text.func = blanks.spots)
> 
> I obtained this error :
> Error in strsplit(x, as.character(split), as.logical(extended)) : 
>         non-character argument in strsplit()
> 
> Does anybody know how to handle this problem? 
> I would really like to use the function maPlot because I would like to keep
> the 'highlighted spots' on the graph(nonrealizable (?) thing with the
> function plot)
>  
> 
> Best regards,
> 
> 
> Francis
> 
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