[BioC] affyPLM - cant plot chip pseudo image

[Rebecca]

Hello,
I have some R/BioC code that was working and is not working any more, and I
suspect that it has to do with the fact that I did a global "update
packages". The error comes from trying to create a pseudo image of a CEL
file which is part of an Affy batch, exactly as is done in the vignette
"affyPLM: Model Based QC Assessment of Affymetrix".

> aBatRef <- ReadAffy()
> Pset <- fitPLM(aBatRef)
> image(Pset, which =2)

Erreur dans image.default(Pset) : argument must be matrix-like


I found a similar problem in the BioC help archives and the asker was
advised to reinstall R, BioC , and all packages. 
So I reinstalled everything with the latest stable versions of R and BioC
and I still get the error.

Looking in the source code for image.R, I see that his particular error is
reported when the dimensions of the objet received are null, and indeed that
is the case: 

> dim(Pset)
NULL

> class(Pset)
[1] "PLMset"
attr(,"package")
[1] "affyPLM"
 
So I tried to use the "Dilution" data set as described in the vignette
"affyPLM: Model Based QC Assessment of Affymetrix" (April 25, 2007). The
only change in the last year to the vignette (with respect to creation of
the pseudo image) is the use of "updateObject"

library(affyPLM)
data(Dilution)
Dilution = updateObject(Dilution)
Pset <- fitPLM(Dilution)
image(Pset, which = 2)

The "Dilution" data set also results in the same error, so I thought that I
would report it to you !  Do you reproduce this ???

Also, in the fitPLM vignette, the examples were "not run" (I have never seen
that before :) 
	Examples
	data(affybatch.example)
	Pset <- fitPLM(affybatch.example,model=PM ~ -1 + probes + samples)
	se(Pset)[1:5,]

	# A larger example testing weight image function
	data(Dilution)
	## Not run: Pset <- fitPLM(Dilution,model=PM ~ -1 + probes +
samples)
	## Not run: image(Pset)
	## Not run: NUSE(Pset) # NUSE

 
Thanks for your help.
PS - I also tried this : image(Pset at residualSE). I get an image but it is
definitely NOT what I was expecting!


> sessionInfo()
R version 2.5.1 (2007-06-27) 
i386-pc-mingw32 

locale:
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French
_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252

attached base packages:
[1] "grDevices" "datasets"  "splines"   "graphics"  "stats"     "utils"
"tools"     "methods"   "base"     

other attached packages:
 hgu95av2cdf mouse4302cdf RColorBrewer      affyPLM        gcrma
matchprobes     affydata   simpleaffy   genefilter     survival 
    "1.16.0"     "1.16.0"      "0.2-3"     "1.12.0"      "2.8.1"
"1.8.1"     "1.11.2"    "2.10.31"     "1.14.1"       "2.32" 
        affy       affyio      Biobase 
    "1.14.2"      "1.4.1"     "1.14.1"