[BioC] Making a PD package for Oligo

[Colleen Doherty]

Duh!  I switched file1 and file2- works great now-
THANKS!

On 10/5/07, Colleen Doherty <colleen.doherty at gmail.com> wrote:
> 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
>


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