[BioC] gcrma problem

[Wenqiong Chen]

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.
Thanks!
wenqiong
.

-----Original Message-----
From: Zhijin Wu [mailto:zwu at jhsph.edu] 
Sent: Tuesday, March 29, 2005 6:20 AM
To: Wenqiong Chen
Cc: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] gcrma problem

You can see the content of function compute.affinities by 
>compute.affinities
#let cdfname be your chip type and
cdfname=cdfName(Scoe.m600.exp)
verbose=TRUE
## then you can run the content of the function and see where the error happens

On Mon, 28 Mar 2005, Wenqiong Chen wrote:

> Hi, list:
> I encountered the following problem when I was running gcrma:
> 
> > gcrma.m600<-gcrma(Scoe.m600.exp)
> Computing affinities.Error in compute.affinities(cdfName(object),
> verbose = verbose) : 
>         NAs are not allowed in subscripted assignments
> 
> How can I find out where the problem occurred?
> Thanks,
> wenqiong
> 
> 
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