[BioC] ReadAffy Error: new versions causing problems?

[James W. MacDonald]

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:
> 
> 
>>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.

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

list.celfiles()?

Also, does

raw <- ReadAffy(filenames=list.celfiles())

help?

Best,

Jim


> 
> 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:
> [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
> 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.
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


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