[BioC] gcrma problem

Wenqiong Chen wenchen at diversa.com
Tue Mar 29 21:55:18 CEST 2005

This is something which frustrates me again!
Yes, I did do "R CMD INSTALL" from the dos command line, and I can clearly see that the package is in the R library. 
Regarding the naming issue, I did not specify anything. Right now, the two packages I built in the library is "disdiv712acdf", and "disdiv712aprobe". Looks pretty consistent.
There is clearly something not trivial there which caused the problem, maybe related to my computer? I am going to give a try in the unix system and see what happens.
Thanks a lot for your help!

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Tuesday, March 29, 2005 11:38 AM
To: Wenqiong Chen
Cc: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] gcrma problem

Wenqiong Chen wrote:
> O.K, here is the step where the error started to occur when I run the 
> content of the function "compute.affinities".. "
>> getProbePackage(probepackagename)
> [1] "Checking to see if your internet connection works..." Error in 
> install.packages2(probepackage, lib = lib) : recursive default 
> argument reference " Alternatively, when I use:
>> getProbePackage(disdiv712aprobe)		#disdiv712aprobe is the
>> probepackagename
> Warning messages: 1: the condition has length > 1 and only the first 
> element will be used in: if (package %in% c("ctest", "eda", "modreg", 
> "mva", "nls", "stepfun", 2: the condition has length > 1 and only the 
> first element will be used in: if (package == "mle") { 3: the 
> condition has length > 1 and only the first element will be used in:
> if (package == "lqs") { [1] "Checking to see if your internet 
> connection works..." Note: You did not specify a download type.
> Using a default value of: Win32 This will be fine for almost all users
> Error in FUN(X[[2]], ...) : Malformed 'pkgs' parameter " I also 
> noticed that when I execute this line, it attempts to download 
> something from BioConductor.
> As Jim already realized, this is not a public GeneChip, but did adopt 
> a standard Affy design. I made the cdf and probe packages by myself 
> using the functions in BioConductor. The R version I am using is 
> R2.0.1, the gcrma package is from the BioConductor 1.5 release.

The function getProbePackage() is trying to download the probe package from the BioC website because it thinks the correct one is not installed. When you made the cdf and probe packages yourself, did you specify a name for either? If so, this may be the cause of the problem.

In addition, after making the packages, did you install them using R CMD INSTALL? If you didn't install them, then they will not be available for R to use, which is another possibility.

If you are on a *nix machine, installing should be straightforward. If you are on MacOS or Windows, you may need to get some tools. If so, you will need to see the corresponding FAQ on the R-project website.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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