[BioC] Unable to perform GCRMA/RMA with cdf file 'mogene11stv1mmentrezgcdf'

Mon Jun 4 16:52:18 CEST 2012

Hi Trent,
In addition to Jim's comments you also may want to have a look at the suggestions Mike Smith provided some time ago:

http://article.gmane.org/gmane.science.biology.informatics.conductor/32506

Note: I didn't try it myself, so I cannot comment any further on it.

HTH,
Guido

--------------------------------------------------------- 
Guido Hooiveld, PhD 
Nutrition, Metabolism & Genomics Group 
Division of Human Nutrition 
Wageningen University 
Biotechnion, Bomenweg 2 
NL-6703 HD Wageningen 
the Netherlands 
tel: (+)31 317 485788 
fax: (+)31 317 483342 
email:      guido.hooiveld at wur.nl
internet:   http://nutrigene.4t.com 
http://scholar.google.com/citations?user=qFHaMnoAAAAJ
http://www.researcherid.com/rid/F-4912-2010

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of James W. MacDonald
Sent: Monday, June 04, 2012 16:31
To: Trent Simmons
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Unable to perform GCRMA/RMA with cdf file 'mogene11stv1mmentrezgcdf'

Hi Trent,

On 6/4/2012 10:14 AM, Trent Simmons wrote:
> Hi All,
>
> I am trying to perform a GCRMA normalization of microarray data that was run on Mouse Gene 1.1 Affymetrix arrays.  I am running into an issue with the CDF file for that array (the CDF file is mogene11stv1mmentrezgcdf).
>
> I obtained the latest version of the CDF file from Brainarray.  When I attempted to perform the compute.affinities step, the error message:
>
> .Error in tmp.exprs[pmIndex[subIndex]] = apm :
>    NAs are not allowed in subscripted assignments
>
> is returned.  Is anyone else experiencing this issue, or have any suggestions for how to resolve it?

The default for gcrma() is to use the MM probes to estimate GC-specific background estimates. However, the Gene ST chips are PM-only chips. 
However, there is an argument to gcrma (NCprobe) that you can use to point to the negative control probes.

>
> I have also tried to perform basic RMA analysis using one of my CEL files and the same CDF file, just in case it was an issue solely with GCRMA.  RMA didn't work either, but in this case, it seems to be that the RMA script is looking for a CDF file called 'mogene11stv1cdf' instead.  Once again, anyone else with this issue or suggestions for a fix?

See the cdfname argument to ReadAffy.

Best,

Jim

>
>
> Thanks in advance,
>
> Trent
>
> ### START CODE ###
> ### LOAD LIBRARIES ###
> library(affy)
> library(gcrma)
> library(AnnotationDbi)
> library(mogene11stv1mmentrezgcdf)
> library(mogene11stv1mmentrezgprobe)
>
>> ### RUN GCRMA ###
>> compute.affinities('mogene11stv1mmentrezg', verbose = TRUE)
> Computing affinities.Error in tmp.exprs[pmIndex[subIndex]] = apm :
>    NAs are not allowed in subscripted assignments
>> traceback()
> 1: compute.affinities("mogene11stv1mmentrezg", verbose = TRUE)
>
>> ### RUN RMA ###
>> setwd('~/Documents/test/mouse/CEL')
>>
>> data<- ReadAffy()
>> eset<- rma(data)
> Error in getCdfInfo(object) :
>    Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MoGene-1_1-st-v1 Library - 
> package mogene11stv1cdf not installed Bioconductor - mogene11stv1cdf 
> not available
>> traceback()
> 12: stop(paste("Could not obtain CDF environment, problems encountered:",
>          paste(unlist(badOut), collapse = "\n"), sep = "\n"))
> 11: getCdfInfo(object)
> 10: .local(object, which, ...)
> 9: indexProbes(object, "pm", genenames = genenames)
> 8: indexProbes(object, "pm", genenames = genenames)
> 7: .local(object, ...)
> 6: pmindex(object, genenames)
> 5: pmindex(object, genenames)
> 4: .local(object, ...)
> 3: probeNames(object, subset)
> 2: probeNames(object, subset)
> 1: rma(data)
>> ### SESSION INFO ###
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
>   [5] LC_MONETARY=en_CA.UTF-8    LC_MESSAGES=en_CA.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] mogene11stv1mmentrezgprobe_15.1.0 mogene11stv1mmentrezgcdf_15.1.0
> [3] AnnotationDbi_1.18.1              gcrma_2.28.0
> [5] BiocInstaller_1.4.6               affy_1.34.0
> [7] Biobase_2.16.0                    BiocGenerics_0.2.0
>
> loaded via a namespace (and not attached):
>   [1] affyio_1.24.0         Biostrings_2.24.1     DBI_0.2-5
>   [4] IRanges_1.14.3        preprocessCore_1.18.0 RSQLite_0.11.1
>   [7] splines_2.15.0        stats4_2.15.0         tools_2.15.0
> [10] zlibbioc_1.2.0
>
> ## END CODE ##
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099

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