[BioC] ReadAffy for moe430acdf

[Margaret Gardiner-Garden]

Hi,

I was wondering if anyone might have some ideas as to why I might be having
a problem using ReadAffy with the mouse chip moe430acdf.


I get the same error whether I use my cel files or cel files downloaded from
the web.  An example file is a cel file umass_A1D0-430A-1[1].CEL.zip which I
downloaded from the web
http://www.diabetesgenome.org/cgi-bin/chipperdb/expt.cgi?id=61 , unzipped
and put it in same directory from which I was running R.

Below I have put the commands, error and traceback for reading the single
file from the web.

>ReadAffy(file="umass_A1D0-430A-1.CEL")


Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) :
        invalid object for as.environment
AffyBatch object
size of arrays=712x712 features (3965 kb)
cdf=MOE430A (??? affyids)
number of samples=1
Error in as.environment(get(cdfname, inherits = FALSE, envir = where)) :
        invalid object for as.environment
In addition: Warning message:
missing cdf environment ! in: show(list())

> traceback()
10: cdfFromEnvironment(cdfname, cur$where, verbose)
9: switch(cur$what, environment = cdfFromEnvironment(cdfname, cur$where,
       verbose), data = cdfFromData(cdfname, cur$where, verbose),
       libPath = cdfFromLibPath(cdfname, cur$where, verbose = verbose),
       bioC = cdfFromBioC(cdfname, cur$where, verbose))
8: getCdfInfo(object)
7: geneNames(object)
6: geneNames(object)
5: cat("number of genes=", length(geneNames(object)), "\n", sep = "")
4: show(list())
3: show(list())
2: print.default(list())
1: print(list())
>
I got the error using R version 2.0.1 and the release version of Affy,
reposTools and Biobase
(see following sessionInfo)

>sessionInfo()
R version 2.0.1, 2004-11-15, i386-pc-mingw32

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
moe430acdf       affy reposTools    Biobase
   "1.4.3"  "1.5.8-1"   "1.5.12"    "1.5.5"


I then tried again with the latest R version 2.1.0 and the developmental
versions of the packages and got the same error.

> sessionInfo()
R version 2.0.1, 2004-11-15, i386-pc-mingw32

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"

other attached packages:
moe430acdf       affy reposTools    Biobase
   "1.4.3"    "1.6.4"   "1.5.15"    "1.5.7"

My machine is Windows XP Professional Version 2002.

I have now uninstalled all my old versions of R in case something was
interfering and have reinstalled R version 2.1.0 but I still have the same
error.

I would really appreciate any advice concerning what may be happening
here!!!

Regards
Marg

Dr Margaret Gardiner-Garden
Garvan Institute of Medical Research
Sydney Australia