[BioC] affyPLM - cant plot chip pseudo image

[James W. MacDonald]

Hi Rebecca,

Rebecca wrote:
> 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
>   

This error indicates that you are not getting the correct method for 
your PLMset object, which indicates some problem with your installation. 
If you load the affyPLM package and type

showMethods("image", class="PLMset")

do you get this?

 > showMethods("image", class="PLMset")
Function: image (package graphics)
x="PLMset"




>
> 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.
>   

How did you re-install? Did you use biocLite() directly, or did you do 
an update.packages()?

Best,

Jim


> 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"
>
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>   



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