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
I changed the argument from
Mm430_Mm_ENTREZG
tomm430mmentrezg
and removed the line to rename the slot that contains the CDF name, but still get error: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.
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:
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).
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:
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
andR CMD install mm430mmentrezgcdf
.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?