User: Walter Jessen

gravatar for Walter Jessen
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Posts by Walter Jessen

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Answer: A: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... 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 t ...
written 10 months ago by Walter Jessen90
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Comment: C: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... 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. ...
written 10 months ago by Walter Jessen90
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Comment: C: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... 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/Vers ...
written 10 months ago by Walter Jessen90
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Comment: C: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... 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" ...
written 10 months ago by Walter Jessen90
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Comment: C: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... Deleted and reinstalled the affy library. No change, same error. ...
written 10 months ago by Walter Jessen90
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Comment: C: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... 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,celfil ...
written 10 months ago by Walter Jessen90 • updated 10 months ago by RamRS24k
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Comment: C: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... Added, but still get the same error. library(mm430mmentrezgcdf,lib.loc='/Library/Frameworks/R.framework/Versions/3.5/Resources/library/mm430mmentrezg') ...
written 10 months ago by Walter Jessen90
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Error in get(cdfname, object 'mm430mmentrezgcdf' not found
... 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: Er ...
rma affy cdf affymetrix written 10 months ago by Walter Jessen90
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Comment: C: Resources To Batch Map Long Gene Names To Entrez Ids?
... Ah, I see. Excellent! Thanks Pierre! ...
written 8.0 years ago by Walter Jessen90
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Comment: C: Resources To Batch Map Long Gene Names To Entrez Ids?
... Thanks Pierre. However, I don't see how this supports batch submissions -- I typically have several hundred names to map. ...
written 8.0 years ago by Walter Jessen90

Latest awards to Walter Jessen

Scholar 10 months ago, created an answer that has been accepted. For A: Error in get(cdfname, object 'mm430mmentrezgcdf' not found
Great Question 8.0 years ago, created a question with more than 5,000 views. For Using R To Perform Statistical Tests On Microarray Data And Cluster The Results
Good Question 8.0 years ago, asked a question that was upvoted at least 5 times. For Using R To Perform Statistical Tests On Microarray Data And Cluster The Results
Popular Question 8.0 years ago, created a question with more than 1,000 views. For Resources To Batch Map Long Gene Names To Entrez Ids?
Autobiographer 8.0 years ago, has more than 80 characters in the information field of the user's profile.
Student 8.4 years ago, asked a question with at least 3 up-votes. For Using R To Perform Statistical Tests On Microarray Data And Cluster The Results
Popular Question 8.4 years ago, created a question with more than 1,000 views. For Using R To Perform Statistical Tests On Microarray Data And Cluster The Results

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