[BioC] ReadAffy Error: new versions causing problems?
boel.brynedal at ki.se
Thu May 24 15:38:09 CEST 2007
Thank you, this works!
On Wed, 2007-05-23 at 11:58 -0400, James W. MacDonald wrote:
> Hi Boel,
> 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
> Also, does
> 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)
> > x86_64-unknown-linux-gnu
> > 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
> > SWEDEN
> > Phone: +46 8 585 819 27
> > Fax: +46 8 585 870 80
> > E-mail: boel.brynedal at ki.se
> > _______________________________________________
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> James W. MacDonald, M.S.
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
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