[BioC] gcrma problem

James W. MacDonald jmacdon at med.umich.edu
Tue Mar 29 16:23:37 CEST 2005

Wenqiong Chen wrote:
> Hi, list:
> I encountered the following problem when I was running gcrma:
> 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?

First, you could tell us what versions of R, gcrma, etc you are using, 
as well as what type of chip. If it is a non-standard chip, where did 
you get the cdfenv?

Second, if you are trying to debug yourself, you can start with a 
traceback() after you get the error, which should help pinpoint where 
things went wrong. You can then step through the offending function 
using debug().



> Thanks,
> wenqiong
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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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