[BioC] Making a PD package for Oligo

[James W. MacDonald]

Hi Colleen,

Colleen Doherty 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

This is a pretty simple problem - scan() thinks there should be 6 things 
in the first line of the sequence file, and there are not. You can look 
at the top of the file using the 'head' function at a terminal prompt 
(e.g., head <TheSequenceFileNameHere>), which will print out the first 
10 lines of the file.

What you do about that is another question. It may be that this sequence 
file is different from the other Affy sequence files, and will require a 
fix in makePlatformDesign to accommodate, or you may have a corrupted file.

Best,

Jim


> 
>> 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
> 
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-- 
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