[BioC] ReadAffy Error: new versions causing problems?

Boel Brynedal boel.brynedal at ki.se
Wed May 23 15:27:23 CEST 2007

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:

> raw<-ReadAffy()
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.

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:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"
[7] "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

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