[BioC] gcrma problem

[Wenqiong Chen]

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
tmp.exprs[pmIndex[subIndex]]?

Thanks a lot!
Regards,
wenqiong

-----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]))
search()

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
734-647-5623




------------------------------------------------------------------------------
This email message and any attachments are confidential and ...{{dropped}}