[BioC] ReadAffy Error: new versions causing problems?
James W. MacDonald
jmacdon at med.umich.edu
Wed May 23 17:58:19 CEST 2007
Boel Brynedal wrote:
> Dear List,
> I am a PhD student at Karolinska Institutet in Sweden. I have a problem
> thats been evolving the last couple of days. The net result is that much
> of what I do produces error messages. I'll give an example:
> Error in read.affybatch(filenames = l$filenames, phenoData = l
> $phenoData, :
> VECTOR_ELT() can only be applied to a 'list', not a 'char'
> Is there something wrong with my CEL-files? I exported some of them to
> another computer with the same version of R and packages, and there it
> worked fine.
I don't know that there is anything wrong with your celfiles. This error
usually means that ReadAffy() is sending something wrong to the C code,
most often due to errant passing of arguments as celfile names. However,
in your case this not what I would expect.
What do you get when you do
raw <- ReadAffy(filenames=list.celfiles())
> When I use the biocLite installing route, the installation of both
> tkWidgets and tcltk seams to fail:
> Loading required package: tkWidgets
> Error: package 'tkWidgets' could not be loaded
> In addition: Warning message:
> there is no package called 'tkWidgets' in: library(pkg, character.only =
> TRUE, logical = TRUE, lib.loc = lib.loc)
> Execution halted
> ERROR: execution of package source for 'marray' failed
> ** Removing '/usr/local/lib64/R/library/marray'
> ** Restoring previous '/usr/local/lib64/R/library/marray'
> Could this be the reason for my problems; that old and new versions of
> packages are mixed?
> My sessionInfo():
> R version 2.5.0 (2007-04-23)
> attached base packages:
>  "splines" "tools" "stats" "graphics" "grDevices" "utils"
>  "datasets" "methods" "base"
> other attached packages:
> gcrma matchprobes simpleaffy genefilter survival affy
> "2.8.1" "1.8.1" "2.8.0" "1.14.1" "2.31" "1.14.0"
> affyio Biobase
> "1.4.0" "1.14.0"
> Or can it be a more general problem? I just installed a new versions of
> both R and bioconductor packages.
> I'm not an expert in Linux or R, so I'll appreciate any advice!
> Thank you,
> Boel Brynedal
> Boel Brynedal, MSc, PhD student
> Karolinska Institutet
> Department of Clinical neuroscience
> Karolinska University hospital Huddinge
> Division of Neurology, R54
> 141 86 Stockholm
> Phone: +46 8 585 819 27
> Fax: +46 8 585 870 80
> E-mail: boel.brynedal at ki.se
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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