[BioC] Making a PD package for Oligo

[Colleen Doherty]

Hi,

I am having some problems making a PD package for the Arabidopsis ATH1
expression chip so that I can switch to using Oligo.
I initially tried to use pdInfoBuilder:

 pkg<-new("AffySNPPDInfoPkgSeed", email = "dohert23 at msu.edu", cdfFile
= cdfFile, csvAnnoFile = csvAnno, csvSeqFile = csvSeq)
 but this was unsuccessful -it just creates an empty file with no warnings.

Trying to make a package with that gives this:
makePdInfoPackage(pkg, destDir=".")Creating package in ./pd.ath1.121501
Error in gsub(nm[i], symbolValues[[i]], res) : invalid argument

 possibly because I was using the wrong class since this is not an SNP chip?

So I switched to the makePlatformDesign package and got this:

makePDpackage("ATH1-121501.CDF", file1=csvSeq, file2= csvAnno,
manufacturer="affymetrix", type="expression")
affymetrix expression
The package will be called pd.ath1.121501
Reading CDF File
Error in read.cdffile.list(filename) :
  SET_STRING_ELT() can only be applied to a 'character vector', not a 'list'

I searched the mailing list and found a similar error:

makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap",file1="Mm_PromPR_v02.cif",manufacturer="affymetrix",
type="tiling")
> affymetrix tiling
> The package will be called pd.mm.prompr.v01.ncbiv35
> Error in makeBPMAPenv(designFile, file1, genomebuild = genomebuild) :
>         SET_VECTOR_ELT() can only be applied to a 'list', not a 'NULL'

but it looks like this was a windows specific error that was solved by
upgrading and I think have updated everything (sessionInfo below).  So
I am guessing that my error is that my files are entered incorrectly
or something (they are all in the working directory)

I know Benilton (and probably many others) have already made this for
the ATH1 chip, so obtaining a copy of that would be a short term fix,
but I would also like to know what I am doing incorrectly in either
(or both) packages.

Thanks,
Colleen


sessionInfo below:

R version 2.6.0 (2007-10-03)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] makePlatformDesign_1.2.0 affyio_1.4.1             oligo_1.2.0
 [4] oligoClasses_0.99.5      affxparser_1.9.5         AnnotationDbi_0.99.24
 [7] preprocessCore_0.99.22   RSQLite_0.6-3            DBI_0.2-3
[10] Biobase_1.14.1

loaded via a namespace (and not attached):
[1] rcompgen_0.1-15

-- 
Colleen Doherty
Thomashow Lab
310 Plant Biology
Michigan State University
East Lansing, MI 48824