Hi there,
I get the following error when running justGCRMA():
eset <- justGCRMA()
Computing affinities.Error in get(nam) : variable "lotus1a520343dim"
was not
found
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
--
Niels H?gslund
BiRC - Bioinformatics Research Center
University of Aarhus
H?egh-Guldbergs Gade 10, Building 1090
DK-8000 Aarhus C, Denmark
Phone +45 8942 3100
Mail: nj at birc.au.dk
Hi Niels,
Niels H?gslund 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