[BioC] affyPLM - cant plot chip pseudo image

[James W. MacDonald]

Rebecca wrote:
> Thank you James,
> Yes, I did use BiocLite to install and got the same results as you for the
> "showMethods". 
> However, after carefully retracing my steps, I now know what I did that
> caused the error, but no idea why, or how to fix it. 
>
> What I did that caused the error was that I put the following line at the
> end of the file "Rprofile.site" in the "~\R-2.5.1\etc" directory 
>
> 	source(file.path(R.home(), "etc", "myRcode.R"))
>   

What is in myRcode.R? Specifically, is there anything in there that 
might affect the class of the PLMset you are producing? What do you get 
from class(Pset)?

Best,

Jim


> Where "myRcode.R" is some code I wrote for an application in R/BioC,
> including the PLMset manipulations. It is in "~\R-2.5.1\etc", next to
> "Rprofile.site".
>
> I put that line in "Rprofile.site" because I would like to be able to
> double-click on the R desktop icon and have R go to the correct directory
> and source the script. In other words, I don't want to have to change the
> working directory and source the code. 
>
> Now when I double click my desk top icon, I get the desired behavior, and my
> home made functions are working except the pseudo image creation from the
> PLMset. As you suggest, it would seem that I am not getting the correct
> method for the PLMset object. 
>
> I noticed that there are two files called "image.R" - one in
> library\graphics and the other in library\marray. It must be defaulting to
> the CRAN one and not the BioC one. But in that case, why would showMethods()
> give the following ? 
> 	> aBat <- ReadAffy()
> 	> Pset <- fitPLM(aBat)
> 	> image(Pset, which =2)
> 	Erreur dans image.default(Pset, which = 2) : argument must be
> matrix-like
> 	> showMethods("image", class="PLMset")
> 	Function: image (package graphics)
> 	x="PLMset"
>
> If you have any advise on how I can get my application to behave correctly,
> I'd really appreciate it. (Rename the BioC version of image.R to something
> unique?)
>
> Thanks again for your kind help.
>
>   
>> 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:
> mouse4302cdf RColorBrewer      affyPLM        gcrma  matchprobes
> affydata   simpleaffy   genefilter     survival         affy 
>     "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"     "1.14.2" 
>       affyio      Biobase 
>      "1.4.1"     "1.14.1"
>
>
>
>
>   



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