Error in get(cdfname, object 'mm430mmentrezgcdf' not found

Question

[Walter Jessen]

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_9.0.1.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

Environment: macOS High Sierra, R version 3.5.1

Here's the code I'm using.

library(affy)
library(mm430mmentrezgcdf)
celpath="/path/to/cel/files"
data=ReadAffy(verbose=TRUE,celfile.path=celpath)
data@cdfName<-"Mm430_Mm_ENTREZG"
data.rma = rma(data)

Any help would be appreciated.

[Ram]

This is a pure R question. Have you tried specifying lib.loc= the dir path where you installed the custom library?

[Walter Jessen]

Added, but still get the same error.

library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mm430mmentrezg')

[Walter Jessen]

This appears to be an issue with the Affy library. I tried another function (justRMA) and get a similar error:

Error in just.rma(filenames = l$filenames, phenoData = l$phenoData, description = l$description,  : 
  object 'mm430mmentrezgcdf' not found
data.rma=justRMA(verbose=TRUE,celfile.path=celpath,cdfname=mm430mmentrezgcdf)

[cpad0112]

try reinstalling affy library and see if the issue goes away.

[Walter Jessen]

Deleted and reinstalled the affy library. No change, same error.

[Santosh Anand]

Why didn't you try the 10.0 CDF

http://bioconductor.org/packages/2.1/data/annotation/html/mm430mmentrezgcdf.html

[Walter Jessen]

Thanks for catching the version error Santosh. Deleted, built and installed from source the 10.0 CDF. No change, same error.

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)

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

[Santosh Anand]

I've the feeling that there is some issue with the names. You may check these things:

1. what does the following line load (check in a fresh r session by doing ls())

   library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mm430mmentrezgcdf')
   

Is that the same as "Mm430_Mm_ENTREZG". If not, change the cdfname argument accordingly.

1. Alternatively, try without passing any cdfname argument (and no data@cdfname). ReadAffy should guess it correctly.

[Walter Jessen]

Both libraries load without error – ls() doesn't reflect anything. I also ran BiocInstaller::biocValid(), which reports that my packages are of the correct version.

> library(affy)
> ls()
character(0)
> library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mm430mmentrezgcdf')
> ls()
character(0)
> BiocInstaller::biocValid()
[1] TRUE

To my knowledge, Mm430_Mm_ENTREZG is the same. The MBNI page uses a HS133A array as an example (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download_v10.asp).

If I drop the cdfname argument, I can RMA the affybatch object.

[Santosh Anand]

Then, it solves the problem by dropping the cdf file. Ain't it? Moreover, you can check what the name of the cdf file used by checking the cdfName slot

[Walter Jessen]

It doesn't solve the problem. Rather, I believe it points to the rma function as the issue. If I rma without identifying the cdfname, the cdf used is Mouse4302. I need to use the custom cdf Mm430_Mm_ENTREZG.

Answer 1

[Walter Jessen]

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 to all suggestions!

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.

[Santosh Anand]

That's great that it got resolved. You may mark your own answer as accepted so as to close this thread.