[BioC] GCRMA Error

[Zhijin Wu]

Hi Guido,
   Thank you very much for getting to this before I did.

Denise,
   Please let me know if matching the CDF and probe packages versions 
solves your problem.

Jean

Hooiveld, Guido wrote:
> Hi again,
> 
> Also, I just noticed from your sessionInfo, the version of the remapped
> CDF (hgu133plus2hsentrezgcdf_11.0.1) and probe
> (hgu133plus2hsentrezgprobe_12.0.0) files do not match. One is from the
> v11 release, the other from v12. I think that is *really* causing the
> problem your facing.
> 
> Guido
> 
>  
> 
>> -----Original Message-----
>> From: bioconductor-bounces at stat.math.ethz.ch 
>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Zhijin Wu
>> Sent: 17 November 2009 05:58
>> To: Denise Mauldin
>> Cc: bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] GCRMA Error
>>
>> 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_N
>> AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
>>> FICATION=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
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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>> Search the archives: 
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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