Question: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
0
gravatar for Walter Jessen
29 days ago by
Walter Jessen90 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_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.

affymetrix cdf affy rma • 209 views
ADD COMMENTlink modified 27 days ago • written 29 days ago by Walter Jessen90

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

ADD REPLYlink written 28 days ago by RamRS19k

Added, but still get the same error.

library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mm430mmentrezg')
ADD REPLYlink written 28 days ago by Walter Jessen90

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)
ADD REPLYlink modified 28 days ago by RamRS19k • written 28 days ago by Walter Jessen90

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

ADD REPLYlink written 28 days ago by cpad011210k

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

ADD REPLYlink written 28 days ago by Walter Jessen90

Why didn't you try the 10.0 CDF

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

ADD REPLYlink written 28 days ago by Santosh Anand4.3k

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

ADD REPLYlink modified 28 days ago • written 28 days ago by Walter Jessen90

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.
ADD REPLYlink modified 28 days ago by RamRS19k • written 28 days ago by Santosh Anand4.3k

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.

ADD REPLYlink written 28 days ago by Walter Jessen90

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

ADD REPLYlink written 28 days ago by Santosh Anand4.3k

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.

ADD REPLYlink written 28 days ago by Walter Jessen90
2
gravatar for Walter Jessen
27 days ago by
Walter Jessen90 wrote:

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.

ADD COMMENTlink written 27 days ago by Walter Jessen90

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

ADD REPLYlink written 26 days ago by Santosh Anand4.3k
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