[BioC] Making a PD package for Oligo

[James W. MacDonald]

In that case ignore the message I just sent ;-D

Jim



Colleen Doherty wrote:
> 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
>>
> 
> 

-- 
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