[BioC] limma Composite Normalisation & Plotting

[Jason Skelton]

Hi All

(using R 1.8.0, limma 1.5.1)


I'm slightly confused with the composite normalisation
which I'm guessing you can only use for positive controls ?


looking at

Message: 3
Date: Thu, 21 Aug 2003 22:04:19 -0400
From: paul.boutros at utoronto.ca
Subject: [BioC] limma: normalizeWithinArrays using composite method
To: bioconductor at stat.math.ethz.ch
Message-ID: <1061517859.3f457a23caac6 at webmail.utoronto.ca>
Content-Type: text/plain; charset=US-ASCII

I've had the same problem:

 >MA.within   <- normalizeWithinArrays(RG, layout, method="composite");

Error in predLoess(object$y, object$x, newx, object$s, object$weights,  :
         NA/NaN/Inf in foreign function call (arg 3)


I've changed the GAL file to include the word CONTROL(in ID column)
next to any controls I have on my array which seems to work when I use:

nwaEXAMPLE <- normalizeWithinArrays(GENEPIXRG, 
LAYOUT,method="composite", controlspots=TRUE)

Is this correct ?
Looking at the code & user guide I'm still confused as to how limma is 
picking up "Control spots" for composite normalization from GAL file or 
elsewhere ?

The arguments describe for normalizeWithinArrays as:
controlspots 	numeric or logical vector specifying the subset of spots 
which are non-differentially expressed control spots, for use with 
method="composite"

Could someone show me an example of both a numeric & logical vector ?

ALSO

When using controlStatus for RGlist & MAlist plots
Can you specify during plotMA(RG) where you want the legend to go ?

using locator() to get appropriate co-ordinates ?

OR would I have to plot the same information by the generic plot() 
function and then use legend(x,y, legend) ?

If so how can I then specify the legend used in the original plotMA ?
& obtain the status colours specified in that plot

Hope that all make sense


thanks for any help


Jason

-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919