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Error in normalize.AffyBatch.invariantset

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Markus Schmidberger ▴ 380

@markus-schmidberger-2240

Last seen 9.6 years ago

Hello, I found a simple error in the "normalize.AffyBatch.invariantset" function. On line 72, there is a "nunlist". I think this should be a unlist! else if (type == "together") { pms <- nunlist(indexProbes(abatch, "both")) do.normalize.Affybatch.invariantset(abatch, pms, prd.td, baseline.type) } Best Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de

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ADD COMMENT • link updated 16.7 years ago by Seth Falcon ★ 7.4k • written 16.7 years ago by Markus Schmidberger ▴ 380

score 0 · Answer 1 · 2007-08-20

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 9.6 years ago

Hi Markus, Markus Schmidberger <schmidb at="" ibe.med.uni-muenchen.de=""> writes: > Hello, > > I found a simple error in the "normalize.AffyBatch.invariantset" > function. On line 72, there is a "nunlist". I think this should be a unlist! > > else if (type == "together") { > pms <- nunlist(indexProbes(abatch, "both")) > do.normalize.Affybatch.invariantset(abatch, pms, prd.td, > baseline.type) > } Thanks for the report. This was fixed in the development version of the affy package on 10 May. The fix applied was: --- a/affy/R/normalize.invariantset.R +++ b/affy/R/normalize.invariantset.R @@ -78,7 +78,7 @@ normalize.AffyBatch.invariantset <- function(abatch, prd.td=c( pms <- unlist(mmindex(abatch)) do.normalize.Affybatch.invariantset(abatch, pms, prd.td, baseline.type) } else if (type == "together"){ - pms <- nunlist(indexProbes(abatch,"both")) + pms <- unlist(indexProbes(abatch,"both")) do.normalize.Affybatch.invariantset(abatch, pms, prd.td, baseline.type) } else if (type == "separate"){ pms <- unlist(pmindex(abatch)) I hope you will continue to send such reports to the list, but when you do, please remember to include package name, version number, R version, etc. Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/

ADD COMMENT • link 16.7 years ago Seth Falcon ★ 7.4k

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Hi, here the missing information: > sessionInfo() R version 2.5.1 (2007-06-27) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: affy affyio Biobase "1.14.2" "1.4.1" "1.14.1" Best, Markus Seth Falcon schrieb: > Hi Markus, > > Markus Schmidberger <schmidb at="" ibe.med.uni-muenchen.de=""> writes: > >> Hello, >> >> I found a simple error in the "normalize.AffyBatch.invariantset" >> function. On line 72, there is a "nunlist". I think this should be a unlist! >> >> else if (type == "together") { >> pms <- nunlist(indexProbes(abatch, "both")) >> do.normalize.Affybatch.invariantset(abatch, pms, prd.td, >> baseline.type) >> } >> > > Thanks for the report. This was fixed in the development version of > the affy package on 10 May. The fix applied was: > > --- a/affy/R/normalize.invariantset.R > +++ b/affy/R/normalize.invariantset.R > @@ -78,7 +78,7 @@ normalize.AffyBatch.invariantset <- function(abatch, prd.td=c( > pms <- unlist(mmindex(abatch)) > do.normalize.Affybatch.invariantset(abatch, pms, prd.td, baseline.type) > } else if (type == "together"){ > - pms <- nunlist(indexProbes(abatch,"both")) > + pms <- unlist(indexProbes(abatch,"both")) > do.normalize.Affybatch.invariantset(abatch, pms, prd.td, baseline.type) > } else if (type == "separate"){ > pms <- unlist(pmindex(abatch)) > > I hope you will continue to send such reports to the list, but when > you do, please remember to include package name, version number, R > version, etc. > > Best, > > + seth > > -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599

ADD REPLY • link 16.7 years ago Markus Schmidberger ▴ 380

score 0 · Answer 2 · 2007-08-20

Hi Markus, Thanks for the report, but Seth beat you to it: ---------------------------------------------------------------------- -- r24575 | sethf | 2007-05-10 10:36:40 -0400 (Thu, 10 May 2007) | 2 lines Changed paths: M /trunk/madman/Rpacks/affy/DESCRIPTION M /trunk/madman/Rpacks/affy/R/normalize.invariantset.R Fix typo in call to unlist (was nunlist). ---------------------------------------------------------------------- -- Best, Jim Markus Schmidberger wrote: > Hello, > > I found a simple error in the "normalize.AffyBatch.invariantset" > function. On line 72, there is a "nunlist". I think this should be a unlist! > > else if (type == "together") { > pms <- nunlist(indexProbes(abatch, "both")) > do.normalize.Affybatch.invariantset(abatch, pms, prd.td, > baseline.type) > } > > Best > Markus > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623