[BioC] Making a PD package for Oligo

[Colleen Doherty]

Hi Benilton,

 Thanks!  Updating affyio fixed the original reason I was trying to
make a new PDpackage in the first place.

Previously, when using read.celfiles in oligo I was getting this error:
Error in .nextMethod(e1, e2)
updating affyio fixed that and I can now use read.celfiles with the
old pd.ath1.121510

I guess I don't need a new PDpackage now, but I still have a problem
making one- if the mistake is obvious to anyone I would appreciate
some advice.


> cdf<-"ATH1-121501.CDF"
> csv<-"ATH1-121501.na23.annot.csv"
> probe<-"ATH1-121501_probe_tab"
> makePDpackage(cdf,file1=csv, file2=probe, manufacturer="affymetrix", type="expression")
affymetrix expression
The package will be called pd.ath1.121501
Reading CDF File
Reading Sequence Info
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
  line 1 did not have 6 elements

> sessionInfo()
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_1.6.0             oligo_1.2.0
 [4] oligoClasses_1.0.0       affxparser_1.10.0        AnnotationDbi_1.0.0
 [7] preprocessCore_1.0.0     RSQLite_0.6-3            DBI_0.2-3
[10] Biobase_1.16.0

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

Thanks,
Colleen