Error in get(cdfname, object 'mm430mmentrezgcdf' not found
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@walter-jessen-18364
Last seen 6.0 years ago

I have some old MOE430_2 CEL files that were previously analyzed using a custom CDF (Brainarray mm430mmentrezgcdf_10.0.0) and I'm trying to duplicate the analysis. I've built and installed the package mm430mmentrezgcdf_10.0.0.tar.gz but when I try to rma the affybatch object, I get the error:

Error in get(cdfname, envir = as.environment(paste("package:", cdfname,  :   object 'mm430mmentrezgcdf' not found

Any help would be appreciated.

Environment: macOS High Sierra 10.13.6, R version 3.5.1, BiocVersion 3.8.0

Here's the code I'm using.

library(affy)
library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mm430mmentrezgcdf')
celpath="/path/to/cel/files"
data=ReadAffy(verbose=TRUE,celfile.path=celpath,cdfname="Mm430_Mm_ENTREZG")
data@cdfName<-"Mm430_Mm_ENTREZG"
data.rma=rma(data)

traceback() and sessionInfo()

> traceback()
13: get(cdfname, envir = as.environment(paste("package:", cdfname, 
        sep = "")))
12: cdfFromLibPath(cdfname, cur$where, verbose = verbose)
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)

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mm430mmentrezgcdf_10.0.0 affy_1.60.0              Biobase_2.42.0           BiocGenerics_0.28.0     

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4    zlibbioc_1.28.0       compiler_3.5.1        tools_3.5.1          
[5] affyio_1.52.0         preprocessCore_1.44.0
affy cdf rma • 1.3k views
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Guido Hooiveld ★ 4.1k
@guido-hooiveld-2020
Last seen 54 minutes ago
Wageningen University, Wageningen, the …

You are calling the ReadAffy function with the wrong argument/name for the CDF. This should be mm430mmentrezg (and not Mm430_Mm_ENTREZG). Also no need to rename the slot that contains the CDF name.

 

Thus:

library(affy)
library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mm430mmentrezgcdf')
celpath="/path/to/cel/files"

data=ReadAffy(verbose=TRUE,celfile.path=celpath,cdfname="mm430mmentrezg")
data.rma=rma(data)

should work...

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I changed the argument from Mm430_Mm_ENTREZG to mm430mmentrezg and removed the line to rename the slot that contains the CDF name, but still get error:

Error in get(cdfname, envir = as.environment(paste("package:", cdfname, : object 'mm430mmentrezgcdf' not found

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I cannot reproduce your error because in R-3.5.1 I cannot get version 10 of the custom CDF installed (due to a namespace error; see below), but apparently you could.

> install.packages("http://bioconductor.org/packages/2.1/data/annotation/src/contrib/mm430mmentrezgcdf_10.0.0.tar.gz",
type='source', repos=NULL)
trying URL 'http://bioconductor.org/packages/2.1/data/annotation/src/contrib/mm430mmentrezgcdf_10.0.0.tar.gz'
Content type 'application/x-tar' length 1750808 bytes (1.7 MB)
downloaded 1.7 MB

* installing *source* package 'mm430mmentrezgcdf' ...
ERROR: a 'NAMESPACE' file is required
* removing 'C:/Program Files/R/R-3.5.1patched/library/mm430mmentrezgcdf'
In R CMD INSTALL
Warning message:
In install.packages("http://bioconductor.org/packages/2.1/data/annotation/src/contrib/mm430mmentrezgcdf_10.0.0.tar.gz",  :
  installation of package ‘D:/TMP/RtmpkXaKIq/downloaded_packages/mm430mmentrezgcdf_10.0.0.tar.gz’ had non-zero exit status
>
>

 

To reproduce the analyses, you have to use R-2.6.x (because the custom CDF v10.0 was released for Bioconductor version 2.1)

 

If you do so, all this is working fine when using some sample MOE430_2 arrays I have laying around:

> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: affyio
Loading required package: preprocessCore
> library(mm430mmentrezgcdf)
>
> celpath="E:\\TEST\\FILES"
>
> data=ReadAffy(verbose=TRUE,celfile.path=celpath,cdfname="mm430mmentrezg")
1 reading E:\\TEST\\FILES/A124_01_FISHOIL.CEL ...instantiating an AffyBatch (intensity a 1004004x33 matrix)...done.
Reading in :E:\\TEST\\FILES/A124_01_FISHOIL.CEL
Reading in : E:\\TEST\\FILES/A124_02_FISHOIL.CEL
<<snip>>
Reading in : E:\\TEST\\FILES/A124_34_CTR.CEL
> data.rma=rma(data)
Background correcting
Normalizing
Calculating Expression
>
> data.rma
ExpressionSet (storageMode: lockedEnvironment)
assayData: 16539 features, 33 samples
  element names: exprs
phenoData
  sampleNames: A124_01_FISHOIL.CEL, A124_02_FISHOIL.CEL, ..., A124_34_CTR.CEL  (33 total)
  varLabels and varMetadata description:
    sample: arbitrary numbering
featureData
  featureNames: 100009600_at, 100012_at, ..., AFFX-TrpnX-M_at  (16539 total)
  fvarLabels and fvarMetadata description: none
experimentData: use 'experimentData(object)'
Annotation: mm430mmentrezg
> sessionInfo()
R version 2.6.1 (2007-11-26)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] mm430mmentrezgcdf_10.0.0 affy_1.16.0              preprocessCore_1.0.0    
[4] affyio_1.6.1             Biobase_1.16.3          
>

 

Bottom line: Installing the very old package (mm430mmentrezgcdf_10.0.0.tar.gz) in the current R/BioC release very likely gives problems, so to really reproduce the previous analysis you'd better revert back to the R/BioC release that was used to generate the data (in this case R-2.6.x /BioC v2.1).

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Entering edit mode

Thank you Guido! I built and installed version 10 of the custom CDF manually, but the problem here apparently stemmed from the rma function in the latest version of BioC. Reverting to R 2.6.x and BioC v2.1 (which used an older version of the script) fixed the issue, and I was able to rma the affybatch object. Many thanks!

Code used:

library(affy)
library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/2.6/Resources/library/mm430mmentrezgcdf')
celpath="/path/to/cel/files"
data=ReadAffy(verbose=TRUE,celfile.path=celpath,cdfname="mm430mmentrezg")
data.rma=rma(data)

The mm430mmentrezg CDF source (downloaded here: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v10.asp) was built and installed via the command line using R CMD build mm430mmentrezgcdf and R CMD install mm430mmentrezgcdf.

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0
Entering edit mode

What is this mm430 array? Do you perhaps mean the mouse430mmentrezgcdf? You seem to think it's installed (you do give a path to the library dir), but R begs to differ. Is that an aspirational path, or do you actually have something installed there?

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