User: lep

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lep90
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Posts by lep

<prev • 16 results • page 1 of 2 • next >
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Answer: A: SCAN.UPC: exception thrown when loading GEOQuery
... RESOLVED - thanks for all of your help.  I solved the RCurl issue (not reading the 64-bit .dll file) by totally uninstalling all R versions from the Windows operating system, as well as removing R-Studio.   I think a lot of things got piled up and created the issue, because when I started with a cle ...
written 4.4 years ago by lep90
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Comment: C: SCAN.UPC: exception thrown when loading GEOQuery
... Sorry, I didn't paste my real celfilepath but rather used "...(   )" I loaded bioC in R, then loaded SCAN.UPC and it's throwing an exception when reading the 64-bit RCurl.dll in the 64-bit library folder for the RCurl package.  (if RCurl is running via SCAN.UPC w/o issues in your win OS, why did so ...
written 4.4 years ago by lep90
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Comment: C: SCAN.UPC: exception thrown when loading GEOQuery
... Sorry, I didn't paste my real celfilepath but rather used "...(   )" I loaded bioC in R, then loaded SCAN.UPC and it's throwing an exception when reading the 64-bit RCurl.dll in the 64-bit library folder for the RCurl package.  (if RCurl is running via SCAN.UPC w/o issues in your win OS, why did so ...
written 4.4 years ago by lep90
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Comment: C: SCAN.UPC: exception thrown when loading GEOQuery
... ...more progress.  Must use lower case "scan" rather than SCAN in the normalizing command syntax.  Now the only error message is: > normalized <- scan(celFilePath) Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file 'C:. ...
written 4.4 years ago by lep90
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Comment: C: SCAN.UPC: exception thrown when loading GEOQuery
... A little progress, used "biocLite('SCAN.UPC') and package loading succeeded.   However, the exception can't find function 'SCAN' appears (see below): > biocLite("SCAN.UPC") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.1. Installing p ...
written 4.4 years ago by lep90
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Comment: C: SCAN.UPC: exception thrown when loading GEOQuery
... Thanks, I went back to R-3.0.1, and just installed RCurl in R by itself, and it loaded fine.   FYI - Using R-Studio and the syntax "library('RCurl')" works fine by itself as well.  It's only when library('SCAN.UPC') is invoked in R-Studio when the u+nsuccessful loading of GEOQuery occurs --> due ...
written 4.4 years ago by lep90
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Comment: C: SCAN.UPC: exception thrown when loading GEOQuery
... Thanks for the tip.  Downloaded windows binaries for RCurl and pasted in the folder structure.   However, the exception is still being thrown.  Was able to successfully run SCAN.UPC a while ago, so the likely issue now is a changed dependency. Any way to go back to earlier versions in order to avoid ...
written 4.4 years ago by lep90
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SCAN.UPC: exception thrown when loading GEOQuery
... I am using Win XP-64, have everything updated (R-3-1-2, BioC, and R-Studio).  When loading package SCAN.UPC, there is an exception being thrown regarding GEOQuery.  I checked if the .dll exist in the 64-bit library for RCurl, and it is present.  Any suggestions? Below is the run code and error mess ...
geoquery scan.upc rcurl written 4.4 years ago by lep90
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Clusplot - changing cluster labels
... There does not seem to be an option for changing the text used for cluster labels, so is there a workaround? I can change the dimnames of the centers (see below), but they don't appear in the graphic (only 1,2,3,4 appear). dimnames(fit$centers)[[1]] <- c("ER", "HER2","LUMA","LUMB") > dimname ...
written 5.3 years ago by lep90
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PAM-50 genefu example with Hu-133A GEO datasets
... Are there any online tutorials (documents) for implementing genefu to perform subtype class prediction using several e.g. Hu-133A GEO breast ca datasets? Thx, LP Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Nam ...
genefu written 5.5 years ago by lep90 • updated 5.5 years ago by Benjamin Haibe-Kains10

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