User: Barry Henderson

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Posts by Barry Henderson

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A2R for Windows or alternative to cutree.order for windows OS
... Has anyone recompiled/ported the A2R library from http://addictedtor.free.fr/index.html to a windows? Alternatively is there a comparable function to cutree.order from A2R available in another library? Thanks Barry ...
written 12.1 years ago by Barry Henderson250
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Answer: A: Triplicate printing and limma
... Not an expert but I have done this for a custom array with duplicates. Limma can deal with replicate spots that are evenly spaced (ndups and spacing functions in the correlation. Either all of your duplicates are adjascent or spaced by some regular number of interveining spots. I simply duplicate o ...
written 12.2 years ago by Barry Henderson250
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Answer: A: ABPkgBuilder Error; Again: Solved
... ARRRRGGHHH.....I just this minute finished installing the final package! Seriously though, thanks! Before I jump, any chance this version fixes the KEGG problems? Tx Barry -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch ...
written 12.3 years ago by Barry Henderson250
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ABPkgBuilder Error; Again: Solved
... Problem solved based on a little more info using Rterm. Perl does not like the use of "\\" in path statements. Use "/" instead. Duh. > llMapping <- parseData(eg, eg at accession) Unrecognized escape \R passed through at C:\PROGRA~1\R\RW2011~1\library\AnnBuild er\temp\tempPerl7276.pl line 4 ...
annotation go cancer organism biobase annotate annbuilder process written 12.3 years ago by Barry Henderson250 • updated 12.3 years ago by Seth Falcon7.4k
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ABPkgBuilder Error; Again
... Hi John Just getting back to AnnBuilder after vacation. 1.6.8.5 worked like a champ on Linux with ABPkgBuilder. But I need/would prefer the package on a windows xp system. When I tried the same process on XP, ABPkgBuilder dies complaining about not finding a temp file. I think it may be related ...
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Answer: A: ABPkgBuilder Error;
... I installed the version you sent me on the linux system. Same error. >From the web site: Package: AnnBuilder Description: Processing annotation date from public data repositories and building annoation data packages or XML data documents using the source data. Version: 1.6.8-4 Author: J. Zha ...
written 12.3 years ago by Barry Henderson250
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Answer: A: ABPkgBuilder Error;
... Yes I am sure. The sessionInfo from the linux installation (using the zip you emailed) is: R version 2.1.1, 2005-06-20, i686-pc-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: AnnBuilder a ...
written 12.3 years ago by Barry Henderson250
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Answer: A: ABPkgBuilder Error;
... John et al. I tried AnnBuilder 1.6.8-4 and it solved the "invalid class.." error but it still fails building the package. Results from windows install is below (same results on linux): > library(AnnBuilder) Loading required package: Biobase Loading required package: tools Welcome to Bioconduct ...
written 12.3 years ago by Barry Henderson250
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Answer: A: ABPkgBuilder Error;
... That helped a little but now I get the following error: ... > mySrcUrls <- getSrcUrl("all", "Homo sapiens") > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, + organism = "Homo sapiens", version = "1 ...
written 12.3 years ago by Barry Henderson250
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Answer: A: ABPkgBuilder Error;
... I just tried the same code on an linux system with the same results. R version 2.1.1, 2005-06-20, i686-pc-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: GO AnnBuilder annotate ...
written 12.3 years ago by Barry Henderson250

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