[BioC] GCRMA Error

[Zhijin Wu]

Hi Denise

I'll download the dataset and try to reproduce the error first and get 
back to you

Jean

Denise Mauldin wrote:
> Greetings all,
>
> I'm running gcrma on arrays from GSE9171 and I'm getting the infamous
> 'NAs are not allowed in subscripted assignments' error.
>
>   
>> GSE9171_GPL570_gcrma <- gcrma(GSE9171_GPL570)
>>     
> Adjusting for optical effect..............................Done.
> Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
>   NAs are not allowed in subscripted assignments
>   
>> traceback()
>>     
> 3: compute.affinities(cdfName(object), verbose = verbose)
> 2: bg.adjust.gcrma(object, affinity.info = affinity.info,
> affinity.source = affinity.source,
>        NCprobe = NCprobe, type = type, k = k, stretch = stretch,
>        correction = correction, GSB.adjust = GSB.adjust, rho = rho,
>        optical.correct = optical.correct, verbose = verbose, fast = fast)
> 1: gcrma(GSE9171_GPL570)
>   
>> compute.affinities(cdfname="HGU133Plus2_Hs_ENTREZG", verbose=TRUE)
>>     
> Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
>   NAs are not allowed in subscripted assignments
>
> Is this an error in the HGU133Plus2_Hs_ENTREZG CDF from brainarray?
> Is there something I can do to fix this?
>
> Thanks,
> Denise
>
>   
>> sessionInfo()
>>     
> R version 2.9.1 (2009-06-26)
> 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=C;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] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hgu133plus2hsentrezgprobe_12.0.0 AnnotationDbi_1.6.1
> [3] hgu133plus2hsentrezgcdf_11.0.1   gcrma_2.16.0
> [5] Biostrings_2.12.10               IRanges_1.2.3
> [7] limma_2.18.3                     affy_1.22.1
> [9] Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0        DBI_0.2-4            preprocessCore_1.6.0
> [4] RSQLite_0.7-3        splines_2.9.1        tools_2.9.1
>
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>   


-- 
-------------------------------------------
Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182
http://www.stat.brown.edu/zwu