[BioC] pdInfobuilder - building custom cdf

[Benilton Carvalho]

Can you update your Biostrings and double check that your sequences
include only valid characters (ATCG)?

On 29 November 2010 12:28, Ania Lorenc <lorenc at evolbio.mpg.de> wrote:
> Hello,
>
> I'm preparing a custom cdf for a custom SNP/CNV array. However,without
> success. Could someone suggest what might cause source  this error?
>
> Thanks,
>
> Ania Lorenc
>
> Parsing file: MOUSEDIVm520650.CDF...
> Getting SNP probes...
> Organizing PM probes for SNPs...
> Getting SNP information...
> Organizing PM probes for CNVs...
> Getting sequences for SNPs...
> Getting sequences for CNVs...
> Merging sequence information for SNPs...
> Merging sequence information for CNVs...
> Creating Biostrings objects...
> Error in .charToXString(basetype, x, solved_SEW) : key 32 not in lookup
> table
> Calls: makePdInfoPackage ... XStringSet -> .charToXStringSet ->
> .charToXString -> .Call
> In addition: Warning messages:
> 1: In rm(cols, ok, colsOut, seq) : object 'ok' not found
> 2: In rm(cols, ok, colsOut, seq) : object 'ok' not found
>
> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
>
> locale:
> [1] C/UTF-8/C/C/C/C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
>  [1] pdInfoBuilder_1.14.1 oligo_1.14.0         oligoClasses_1.12.1
>  [4] affxparser_1.22.0    RSQLite_0.9-3        DBI_0.2-5
>  [7] Biobase_2.10.0       R.utils_1.5.7        R.oo_1.7.4
> [10] R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
> [1] Biostrings_2.18.0     IRanges_1.8.2         affyio_1.18.0
> [4] preprocessCore_1.12.0 splines_2.12.0
>>
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.0
>
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