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Last seen 10.2 years ago
Dear All,
I would be grateful if you could provide assistance with a problem I
am experiencing using Bioconductor to analyse Affymetrics microarray
data. I am using the package affylmGUI and have managed to reproduce
volcano plots from both experimental and other test data which have
probe set IDs. This is after normalisation and linear model fitting.
However when I try to apply gene names the error below occurs.
Error in text.default(fit$coef[topGenes],fit$lods[topGenes],
labels=substring(genelist[topGenes, : zero length 'labels'
The volcano plot is produced but with no labels. Also the TopTable
does not contain gene names or functions. This occurs with data files
from two different chips.
I have just started analysing data using R and bioconductor and so
have tried to work this problem but have unfortunately been unable to
resolve the situation.
I am using MacOSX Snow Leopard and would be grateful for any help.
With kindest regards,
Dr Jagtar Singh Nijjar
Clinical Lecturer in Rheumatology
University of Glasgow
-- output of sessionInfo():
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] tcltk stats graphics grDevices utils
[6] datasets methods base
other attached packages:
[1] mogene10stv1cdf_2.9.1 AnnotationDbi_1.16.10
[3] affylmGUI_1.28.0 affyio_1.22.0
[5] affy_1.32.0 Biobase_2.14.0
[7] limma_3.10.0
loaded via a namespace (and not attached):
[1] BiocInstaller_1.2.1 DBI_0.2-5
[3] IRanges_1.12.5 preprocessCore_1.16.0
[5] RSQLite_0.11.1 tools_2.14.0
[7] zlibbioc_1.0.0
Warning messages:
1: The biocReposList() function is deprecated. Please use
biocLite() to install
packages:
source("http://bioconductor.org/biocLite.R")
biocLite("<pkgname>")
If you really need to get the list of Bioconductor package
repositories (like
biocReposList() does), then do:
source("http://bioconductor.org/biocLite.R")
biocinstallRepos()
2: In getDependencies(pkgs, dependencies, available, lib) :
Do not know which element of 'lib' to install dependencies into
skipping dependencies
3: In getDependencies(pkgs, dependencies, available, lib) :
package ???mogene10stv1??? is not available (for R version 2.14.0)
--
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