[BioC] justGCRMA() error message

[James W. MacDonald]

Hi Niels,

Niels Høgslund wrote:
> Hi there,
> 
> I get the following error when running justGCRMA():
> 
> eset <- justGCRMA()
> Computing affinities.Error in get(nam) : variable "lotus1a520343dim" was not
> found

This is an environment that is supposed to be in the cdf package for 
this chip. Did you make the cdf with an older version of makecdfenv? If 
you load the cdf package and then do

ls("package:lotus1a520343cdf")

do you see a lotus1a520343dim listed there?

If not, you need to re-create this package with a current version of 
makecdfenv and re-install.

Best,

Jim


> 
> As shown, I have a custom affy chip named "lotus1a520343". justGCRMA() has not
> been causing me any trouble with this chip and probe package before. Can't
> figure out exactly what goes wrong, I hope somebody can?
> 
> setup:
> 
>> sessionInfo()
> R version 2.6.2 (2008-02-08)
> i686-pc-linux-gnu
> 
> locale:
> C
> 
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> [8] methods   base
> 
> other attached packages:
> [1] affyPLM_1.14.0       gcrma_2.10.0         matchprobes_1.10.0
> [4] affy_1.16.0          preprocessCore_1.0.0 affyio_1.6.1
> [7] Biobase_1.16.3
> 
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-17
> 
> 
> 
> Cheers,
> Niels
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623