[BioC] Making a PD package for Oligo

[Benilton Carvalho]

Hi Colleen,

the pdInfoBuilder will not work just yet... In the (near, I hope)  
future, pdInfoBuilder should handle everything, but for the moment  
only SNP arrays are supported.

So, you're on the right track, use makePlatformDesign. I do remember  
seeing errors like the one you reported and I think upgrading the  
affyio package will fix it. Give that a try and let us know what your  
sessionInfo() is, okay?

best,

b

On Oct 4, 2007, at 1:41 PM, Colleen Doherty wrote:

> 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
>
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