[BioC] gcrma problem

Wenqiong Chen wenchen at diversa.com
Fri Apr 1 00:58:48 CEST 2005

Hi, Jim and Zhijin:
I found the problem with the probe package, and it turned out to be very
much trivial! It is the problem with the quotation, in 
>getProbePackage(disdiv712aprobe), the name of the probe package should
be quoted! :-(

O.K, now, following each step in compute.affinities, I finally came to
the "real" problem in the line
> tmp.exprs[pmIndex[subIndex]] = apm
Error: NAs are not allowed in subscripted assignments

I have checked vector "apm" and there is no NA, and the lengths of apm
and tmp.exprs[pmIndex[subIndex]] are the same. Based on the code right
before this line, the tmp.exprs[pmIndex[subIndex]] has all the NAs. Does
this line try to assign the value from apm to

Thanks a lot!

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Thursday, March 31, 2005 11:24 AM
To: Wenqiong Chen
Cc: Bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] gcrma problem

Wenqiong Chen wrote:
> Hi, Jim:
> Thanks for debugging for me!
> I tried the following commands and got exactly what you have expected.
> Also, I tried everything in the unix system, and got exactly the same 
> error message.
> Wenqiong

Hmmm. What happens if you do this:

do.call("library", list("disdiv712acdf", .libPaths()[1]))
do.call("library", list("disdiv712aprobe", .libPaths()[1]))

Does it list both of the packages after .GlobalEnv?

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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