justGCRMA() error message
1
0
Entering edit mode
@nielshgslund-2694
Last seen 10.5 years ago
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
probe affy probe affy • 571 views
ADD COMMENT
0
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States
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
ADD COMMENT

Login before adding your answer.

Traffic: 512 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6