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Question: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
0
gravatar for Walter Jessen
22 days ago by
Walter Jessen0 wrote:

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
ADD COMMENTlink modified 22 days ago by Guido Hooiveld2.3k • written 22 days ago by Walter Jessen0
1
gravatar for Guido Hooiveld
22 days ago by
Guido Hooiveld2.3k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.3k wrote:

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...

ADD COMMENTlink written 22 days ago by Guido Hooiveld2.3k

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

ADD REPLYlink written 22 days ago by Walter Jessen0
1

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).

ADD REPLYlink modified 22 days ago • written 22 days ago by Guido Hooiveld2.3k

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.

ADD REPLYlink written 21 days ago by Walter Jessen0

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?

ADD REPLYlink written 22 days ago by James W. MacDonald48k
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