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

[James W. MacDonald]

Hi Trent,

On 6/4/2012 10:46 AM, Trent Simmons wrote:
> Hi Jim,
>
> That has solved the RMA issue.  Thank you very much!  Any idea for the GCRMA issue?

Sure, as I noted below, you can use the NCprobes argument to point to 
the negative control probes on the chip. I have no idea if these exist 
on the remapped cdf - it's up to you to figure that part out.

Best,

Jim


>
> Best,
>
> Trent
> ________________________________________
> From: James W. MacDonald [jmacdon at uw.edu]
> Sent: Monday, June 04, 2012 10:30 AM
> 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
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099