[BioC] GCRMA Error

Denise Mauldin dmauldin at systemsbiology.org
Tue Nov 17 18:09:57 CET 2009


That does appear to be the problem.  Is there an easy way to make sure
that something like that doesn't happen again?  I don't recall
installing any of those packages by hand.

Thanks,
Denise

On Tue, Nov 17, 2009 at 8:18 AM, Zhijin Wu <zwu at stat.brown.edu> wrote:
>
> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
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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
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>
>
>
> --
> ------------------------------------
> 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
>
>



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