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Question: Problems with affycomp - quantile.default
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gravatar for Markus Schmidberger
11.0 years ago by
Markus Schmidberger380 wrote:
Hello, I want to do some comparison with affycomp and use the affycompII data. This is my code library(affy) library("affycomp") path <- "/Microarray/hgu95a-spikein/rawdata" celFile <- list.celfiles(path=path,full.names=TRUE); affyBatch <- ReadAffy(filenames=celFile); eset1 <- rma(affyBatch) assessFC(eset1,method.name="RMA.2") and I get the ERROR: Fehler in quantile.default(m[-spikeindex], prob = probs) : missing values and NaN's not allowed if 'na.rm' is FALSE How to fix this? R version 2.5.0 (2007-04-23) i686-pc-linux-gnu locale: LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_DE .UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_DE. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: hgu95acdf affycomp affy affyio Biobase "1.16.0" "1.12.0" "1.14.1" "1.4.0" "1.14.0" Thanks, 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
ADD COMMENTlink modified 11.0 years ago by James W. MacDonald47k • written 11.0 years ago by Markus Schmidberger380
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gravatar for Richard Finney
11.0 years ago by
Richard Finney180 wrote:
I'm getting a mysterious error message "no slot of name "exprs" for this object of class "AffyBatch"" Anybody got any ideas on what crime I committed? I got the latest greatest Bioconductor stuff yesterday. The gory details ... -bash-3.00$ uname -a Linux xxxxx.yyy.nih.gov 2.6.9-42.0.3.ELsmp #1 SMP Mon Sep 25 17:24:31 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux -bash-3.00$ R WARNING: ignoring environment value of R_HOME R version 2.5.1 (2007-06-27) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 ... [blah blah blah ] .... [Previously saved workspace restored] > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio > library(PLASQ500K) Loading required package: GLAD Loading required package: aws [1] "Have fun with GLAD" > pscn(NspFolder=NULL, StyFolder="/work/joe/TUMOR", normNspFolder=NULL, normStyFolder="/work/joe/NORMAL") [1] "Reading in Normal .cel files" [1] "Reading Files" [1] "XMapping250K_Sty_A02_47432.CEL" [1] "now readaffy" Error in round(ReadAffy(filenames = paste(celFolder, i, sep = "/"))@exprs) : no slot of name "exprs" for this object of class "AffyBatch" > ________________________________________________________________ ____________________ Luggage? GPS? Comic books?
ADD COMMENTlink written 11.0 years ago by Richard Finney180
Dear Richard, as has been mentioned on this list before, you will be more likely to get a useful answer if you state the output of "sessionInfo()". Best wishes Wolfgang Finney ha scritto: > I'm getting a mysterious error message > "no slot of name "exprs" for this object of class > "AffyBatch"" > > Anybody got any ideas on what crime I committed? > > I got the latest greatest Bioconductor stuff > yesterday. > > The gory details ... > > -bash-3.00$ uname -a > Linux xxxxx.yyy.nih.gov 2.6.9-42.0.3.ELsmp #1 SMP Mon > Sep 25 17:24:31 EDT 2006 x86_64 x86_64 x86_64 > GNU/Linux > > -bash-3.00$ R > WARNING: ignoring environment value of R_HOME > > R version 2.5.1 (2007-06-27) > Copyright (C) 2007 The R Foundation for Statistical > Computing > ISBN 3-900051-07-0 > ... [blah blah blah ] .... > > [Previously saved workspace restored] > >> library(affy) > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, > type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages > 'citation(pkgname)'. > > Loading required package: affyio >> library(PLASQ500K) > Loading required package: GLAD > Loading required package: aws > [1] "Have fun with GLAD" >> pscn(NspFolder=NULL, StyFolder="/work/joe/TUMOR", > normNspFolder=NULL, normStyFolder="/work/joe/NORMAL") > [1] "Reading in Normal .cel files" > [1] "Reading Files" > [1] "XMapping250K_Sty_A02_47432.CEL" > [1] "now readaffy" > Error in round(ReadAffy(filenames = paste(celFolder, > i, sep = "/"))@exprs) : > no slot of name "exprs" for this object of > class "AffyBatch"
ADD REPLYlink written 11.0 years ago by Wolfgang Huber13k
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gravatar for James W. MacDonald
11.0 years ago by
United States
James W. MacDonald47k wrote:
Hi Markus, Markus Schmidberger wrote: > Hello, > > I want to do some comparison with affycomp and use the affycompII data. > This is my code > > library(affy) > library("affycomp") > path <- "/Microarray/hgu95a-spikein/rawdata" > celFile <- list.celfiles(path=path,full.names=TRUE); > affyBatch <- ReadAffy(filenames=celFile); > eset1 <- rma(affyBatch) > assessFC(eset1,method.name="RMA.2") > > and I get the ERROR: > Fehler in quantile.default(m[-spikeindex], prob = probs) : > missing values and NaN's not allowed if 'na.rm' is FALSE If you look at the code for assessFC(), you will see that the spikeindex comes from the phenoData slot of the ExpressionSet object (in particular the genenames column, which I assume lists the probesets that were spiked in). If you don't have this information in your phenoData slot, then assessFC() won't work, and I assume this to be true of the other assessXX() functions as well. The phenoData can be accessed using data(spikein.phenodata). Unfortunately this is an old-style phenoData object instead of an AnnotatedDataFrame, so you have to update first. pd <- data(spikein.phenodata) pd <- as(pd, "AnnotatedDataFrame") ## you will see warnings here that I think you can ignore affyBatch <- ReadAffy(filenames=celFile, phenoData=pd) should get you going. Best, Jim > > How to fix this? > > R version 2.5.0 (2007-04-23) > i686-pc-linux-gnu > locale: > LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de_ DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_D E.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UTF -8;LC_IDENTIFICATION=C > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "methods" "base" > other attached packages: > hgu95acdf affycomp affy affyio Biobase > "1.16.0" "1.12.0" "1.14.1" "1.4.0" "1.14.0" > > Thanks, > Markus > -- James W. MacDonald, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD COMMENTlink written 11.0 years ago by James W. MacDonald47k
Hello, Phenodata do not help. I changed my code to this: library(affy) library(affycomp) pathRawData <- "~/Microarray/hgu95a-spikein/rawdata" pathPhenoData <- "~/Microarray/hgu95a-spikein/spikein_pdata.txt" celFile <- list.celfiles(path=pathRawData,full.names=TRUE); pd<-read.AnnotatedDataFrame(filename=pathPhenoData, header=TRUE, row.names="filename", sep=" ") affyBatch <- ReadAffy(filenames=celFile, phenoData=pd); eset <- rma(affyBatch) assessFC(eset,method.name="RMA") and I still have the same error: Fehler in quantile.default(m[-spikeindex], prob = probs) : missing values and NaN's not allowed if 'na.rm' is FALSE (same error with the hgu133 dataset) What I have to change? Thanks, Markus James MacDonald schrieb: > Hi Markus, > > Markus Schmidberger wrote: >> Hello, >> >> I want to do some comparison with affycomp and use the affycompII >> data. This is my code >> >> library(affy) >> library("affycomp") >> path <- "/Microarray/hgu95a-spikein/rawdata" >> celFile <- list.celfiles(path=path,full.names=TRUE); >> affyBatch <- ReadAffy(filenames=celFile); >> eset1 <- rma(affyBatch) >> assessFC(eset1,method.name="RMA.2") >> >> and I get the ERROR: >> Fehler in quantile.default(m[-spikeindex], prob = probs) : >> missing values and NaN's not allowed if 'na.rm' is FALSE > > If you look at the code for assessFC(), you will see that the > spikeindex comes from the phenoData slot of the ExpressionSet object > (in particular the genenames column, which I assume lists the > probesets that were spiked in). If you don't have this information in > your phenoData slot, then assessFC() won't work, and I assume this to > be true of the other assessXX() functions as well. > > The phenoData can be accessed using data(spikein.phenodata). > Unfortunately this is an old-style phenoData object instead of an > AnnotatedDataFrame, so you have to update first. > > pd <- data(spikein.phenodata) > pd <- as(pd, "AnnotatedDataFrame") > ## you will see warnings here that I think you can ignore > affyBatch <- ReadAffy(filenames=celFile, phenoData=pd) > > should get you going. > > Best, > > Jim > > >> >> How to fix this? >> >> R version 2.5.0 (2007-04-23) >> i686-pc-linux-gnu >> locale: >> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=de _DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de_ DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.UT F-8;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] "tools" "stats" "graphics" "grDevices" "utils" >> "datasets" >> [7] "methods" "base" other attached packages: >> hgu95acdf affycomp affy affyio Biobase >> "1.16.0" "1.12.0" "1.14.1" "1.4.0" "1.14.0" >> >> Thanks, >> 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 Tel: +49 (089) 7095 - 4599
ADD REPLYlink written 11.0 years ago by Markus Schmidberger380
Are you sure you have the correct phenoData? What do you get from colnames(pData(eset))? You should get this: > colnames(pData(eset)) [1] "37777_at" "684_at" "1597_at" "38734_at" "39058_at" "36311_at" [7] "36889_at" "1024_at" "36202_at" "36085_at" "40322_at" "407_at" [13] "1091_at" "1708_at" "33818_at" "546_at" If you don't, you have the incorrect phenoData, and you should use pd <- as(data(spikein.phenodata), "AnnotatedDataFrame") Best, Jim Markus Schmidberger wrote: > Hello, > > Phenodata do not help. I changed my code to this: > > library(affy) > library(affycomp) > pathRawData <- "~/Microarray/hgu95a-spikein/rawdata" > pathPhenoData <- "~/Microarray/hgu95a-spikein/spikein_pdata.txt" > celFile <- list.celfiles(path=pathRawData,full.names=TRUE); > pd<-read.AnnotatedDataFrame(filename=pathPhenoData, header=TRUE, > row.names="filename", sep=" ") > affyBatch <- ReadAffy(filenames=celFile, phenoData=pd); > eset <- rma(affyBatch) > assessFC(eset,method.name="RMA") > > and I still have the same error: > Fehler in quantile.default(m[-spikeindex], prob = probs) : > missing values and NaN's not allowed if 'na.rm' is FALSE > > (same error with the hgu133 dataset) > > What I have to change? > > Thanks, > Markus > > James MacDonald schrieb: >> Hi Markus, >> >> Markus Schmidberger wrote: >>> Hello, >>> >>> I want to do some comparison with affycomp and use the affycompII >>> data. This is my code >>> >>> library(affy) >>> library("affycomp") >>> path <- "/Microarray/hgu95a-spikein/rawdata" >>> celFile <- list.celfiles(path=path,full.names=TRUE); >>> affyBatch <- ReadAffy(filenames=celFile); >>> eset1 <- rma(affyBatch) >>> assessFC(eset1,method.name="RMA.2") >>> >>> and I get the ERROR: >>> Fehler in quantile.default(m[-spikeindex], prob = probs) : >>> missing values and NaN's not allowed if 'na.rm' is FALSE >> If you look at the code for assessFC(), you will see that the >> spikeindex comes from the phenoData slot of the ExpressionSet object >> (in particular the genenames column, which I assume lists the >> probesets that were spiked in). If you don't have this information in >> your phenoData slot, then assessFC() won't work, and I assume this to >> be true of the other assessXX() functions as well. >> >> The phenoData can be accessed using data(spikein.phenodata). >> Unfortunately this is an old-style phenoData object instead of an >> AnnotatedDataFrame, so you have to update first. >> >> pd <- data(spikein.phenodata) >> pd <- as(pd, "AnnotatedDataFrame") >> ## you will see warnings here that I think you can ignore >> affyBatch <- ReadAffy(filenames=celFile, phenoData=pd) >> >> should get you going. >> >> Best, >> >> Jim >> >> >>> How to fix this? >>> >>> R version 2.5.0 (2007-04-23) >>> i686-pc-linux-gnu >>> locale: >>> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE=d e_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=de _DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE.U TF-8;LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] "tools" "stats" "graphics" "grDevices" "utils" >>> "datasets" >>> [7] "methods" "base" other attached packages: >>> hgu95acdf affycomp affy affyio Biobase >>> "1.16.0" "1.12.0" "1.14.1" "1.4.0" "1.14.0" >>> >>> Thanks, >>> 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
ADD REPLYlink written 11.0 years ago by James W. MacDonald47k
Hi Jim, thanks a lot, now it works. But what is wrong by reading the phenodata-File > pd95<-read.AnnotatedDataFrame(filename="spikein_pdata.txt", header=TRUE, row.names="filename", sep=" ") > colnames(pData(pd95)) [1] "X37777_at" "X684_at" "X1597_at" "X38734_at" "X39058_at" "X36311_at" [7] "X36889_at" "X1024_at" "X36202_at" "X36085_at" "X40322_at" "X407_at" [13] "X1091_at" "X1708_at" "X33818_at" "X546_at" Attached the pdata-File from the affycompII website (http://affycomp.biostat.jhsph.edu/) (set="\t" also does not work) Thanks Markus James W. MacDonald schrieb: > Are you sure you have the correct phenoData? What do you get from > > colnames(pData(eset))? > > You should get this: > > > colnames(pData(eset)) > [1] "37777_at" "684_at" "1597_at" "38734_at" "39058_at" "36311_at" > [7] "36889_at" "1024_at" "36202_at" "36085_at" "40322_at" "407_at" > [13] "1091_at" "1708_at" "33818_at" "546_at" > > If you don't, you have the incorrect phenoData, and you should use > > pd <- as(data(spikein.phenodata), "AnnotatedDataFrame") > > Best, > > Jim > > > > Markus Schmidberger wrote: >> Hello, >> >> Phenodata do not help. I changed my code to this: >> >> library(affy) >> library(affycomp) >> pathRawData <- "~/Microarray/hgu95a-spikein/rawdata" >> pathPhenoData <- "~/Microarray/hgu95a-spikein/spikein_pdata.txt" >> celFile <- list.celfiles(path=pathRawData,full.names=TRUE); >> pd<-read.AnnotatedDataFrame(filename=pathPhenoData, header=TRUE, >> row.names="filename", sep=" ") >> affyBatch <- ReadAffy(filenames=celFile, phenoData=pd); >> eset <- rma(affyBatch) >> assessFC(eset,method.name="RMA") >> >> and I still have the same error: >> Fehler in quantile.default(m[-spikeindex], prob = probs) : >> missing values and NaN's not allowed if 'na.rm' is FALSE >> >> (same error with the hgu133 dataset) >> >> What I have to change? >> >> Thanks, >> Markus >> >> James MacDonald schrieb: >>> Hi Markus, >>> >>> Markus Schmidberger wrote: >>>> Hello, >>>> >>>> I want to do some comparison with affycomp and use the affycompII >>>> data. This is my code >>>> >>>> library(affy) >>>> library("affycomp") >>>> path <- "/Microarray/hgu95a-spikein/rawdata" >>>> celFile <- list.celfiles(path=path,full.names=TRUE); >>>> affyBatch <- ReadAffy(filenames=celFile); >>>> eset1 <- rma(affyBatch) >>>> assessFC(eset1,method.name="RMA.2") >>>> >>>> and I get the ERROR: >>>> Fehler in quantile.default(m[-spikeindex], prob = probs) : >>>> missing values and NaN's not allowed if 'na.rm' is FALSE >>> If you look at the code for assessFC(), you will see that the >>> spikeindex comes from the phenoData slot of the ExpressionSet object >>> (in particular the genenames column, which I assume lists the >>> probesets that were spiked in). If you don't have this information >>> in your phenoData slot, then assessFC() won't work, and I assume >>> this to be true of the other assessXX() functions as well. >>> >>> The phenoData can be accessed using data(spikein.phenodata). >>> Unfortunately this is an old-style phenoData object instead of an >>> AnnotatedDataFrame, so you have to update first. >>> >>> pd <- data(spikein.phenodata) >>> pd <- as(pd, "AnnotatedDataFrame") >>> ## you will see warnings here that I think you can ignore >>> affyBatch <- ReadAffy(filenames=celFile, phenoData=pd) >>> >>> should get you going. >>> >>> Best, >>> >>> Jim >>> >>> >>>> How to fix this? >>>> >>>> R version 2.5.0 (2007-04-23) >>>> i686-pc-linux-gnu >>>> locale: >>>> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE= de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER=d e_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE. UTF-8;LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] "tools" "stats" "graphics" "grDevices" "utils" >>>> "datasets" >>>> [7] "methods" "base" other attached packages: >>>> hgu95acdf affycomp affy affyio Biobase >>>> "1.16.0" "1.12.0" "1.14.1" "1.4.0" "1.14.0" >>>> >>>> Thanks, >>>> 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 Tel: +49 (089) 7095 - 4599 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: spikein_pdata.txt Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070813/ b92a8a61/attachment.txt
ADD REPLYlink written 11.0 years ago by Markus Schmidberger380
Hi Markus, There is an argument to read.table(), 'check.names', that is by default set to TRUE. This argument tells R that you want to ensure that all names are syntactically valid (and a name that starts with a number is not). You can get around that by adding check.names=FALSE to your call to read.AnnotatedDataFrame(): > pd <- read.AnnotatedDataFrame("spikein_pdata.txt", header=TRUE, sep=" ", row.names="filename", check.names=FALSE) > colnames(pData(pd)) [1] "37777_at" "684_at" "1597_at" "38734_at" "39058_at" "36311_at" [7] "36889_at" "1024_at" "36202_at" "36085_at" "40322_at" "407_at" [13] "1091_at" "1708_at" "33818_at" "546_at" Best, Jim Markus Schmidberger wrote: > Hi Jim, > > thanks a lot, now it works. > But what is wrong by reading the phenodata-File > > > pd95<-read.AnnotatedDataFrame(filename="spikein_pdata.txt", > header=TRUE, row.names="filename", sep=" ") > > > colnames(pData(pd95)) > [1] "X37777_at" "X684_at" "X1597_at" "X38734_at" "X39058_at" "X36311_at" > [7] "X36889_at" "X1024_at" "X36202_at" "X36085_at" "X40322_at" > "X407_at" [13] "X1091_at" "X1708_at" "X33818_at" "X546_at" > Attached the pdata-File from the affycompII website > (http://affycomp.biostat.jhsph.edu/) > (set="\t" also does not work) > > Thanks > Markus > > > James W. MacDonald schrieb: >> Are you sure you have the correct phenoData? What do you get from >> >> colnames(pData(eset))? >> >> You should get this: >> >> > colnames(pData(eset)) >> [1] "37777_at" "684_at" "1597_at" "38734_at" "39058_at" "36311_at" >> [7] "36889_at" "1024_at" "36202_at" "36085_at" "40322_at" "407_at" >> [13] "1091_at" "1708_at" "33818_at" "546_at" >> >> If you don't, you have the incorrect phenoData, and you should use >> >> pd <- as(data(spikein.phenodata), "AnnotatedDataFrame") >> >> Best, >> >> Jim >> >> >> >> Markus Schmidberger wrote: >>> Hello, >>> >>> Phenodata do not help. I changed my code to this: >>> >>> library(affy) >>> library(affycomp) >>> pathRawData <- "~/Microarray/hgu95a-spikein/rawdata" >>> pathPhenoData <- "~/Microarray/hgu95a-spikein/spikein_pdata.txt" >>> celFile <- list.celfiles(path=pathRawData,full.names=TRUE); >>> pd<-read.AnnotatedDataFrame(filename=pathPhenoData, header=TRUE, >>> row.names="filename", sep=" ") >>> affyBatch <- ReadAffy(filenames=celFile, phenoData=pd); >>> eset <- rma(affyBatch) >>> assessFC(eset,method.name="RMA") >>> >>> and I still have the same error: >>> Fehler in quantile.default(m[-spikeindex], prob = probs) : >>> missing values and NaN's not allowed if 'na.rm' is FALSE >>> >>> (same error with the hgu133 dataset) >>> >>> What I have to change? >>> >>> Thanks, >>> Markus >>> >>> James MacDonald schrieb: >>>> Hi Markus, >>>> >>>> Markus Schmidberger wrote: >>>>> Hello, >>>>> >>>>> I want to do some comparison with affycomp and use the affycompII >>>>> data. This is my code >>>>> >>>>> library(affy) >>>>> library("affycomp") >>>>> path <- "/Microarray/hgu95a-spikein/rawdata" >>>>> celFile <- list.celfiles(path=path,full.names=TRUE); >>>>> affyBatch <- ReadAffy(filenames=celFile); >>>>> eset1 <- rma(affyBatch) >>>>> assessFC(eset1,method.name="RMA.2") >>>>> >>>>> and I get the ERROR: >>>>> Fehler in quantile.default(m[-spikeindex], prob = probs) : >>>>> missing values and NaN's not allowed if 'na.rm' is FALSE >>>> If you look at the code for assessFC(), you will see that the >>>> spikeindex comes from the phenoData slot of the ExpressionSet object >>>> (in particular the genenames column, which I assume lists the >>>> probesets that were spiked in). If you don't have this information >>>> in your phenoData slot, then assessFC() won't work, and I assume >>>> this to be true of the other assessXX() functions as well. >>>> >>>> The phenoData can be accessed using data(spikein.phenodata). >>>> Unfortunately this is an old-style phenoData object instead of an >>>> AnnotatedDataFrame, so you have to update first. >>>> >>>> pd <- data(spikein.phenodata) >>>> pd <- as(pd, "AnnotatedDataFrame") >>>> ## you will see warnings here that I think you can ignore >>>> affyBatch <- ReadAffy(filenames=celFile, phenoData=pd) >>>> >>>> should get you going. >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>>> How to fix this? >>>>> >>>>> R version 2.5.0 (2007-04-23) >>>>> i686-pc-linux-gnu >>>>> locale: >>>>> LC_CTYPE=de_DE.UTF-8;LC_NUMERIC=C;LC_TIME=de_DE.UTF-8;LC_COLLATE =de_DE.UTF-8;LC_MONETARY=de_DE.UTF-8;LC_MESSAGES=de_DE.UTF-8;LC_PAPER= de_DE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE .UTF-8;LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] "tools" "stats" "graphics" "grDevices" "utils" >>>>> "datasets" >>>>> [7] "methods" "base" other attached packages: >>>>> hgu95acdf affycomp affy affyio Biobase >>>>> "1.16.0" "1.12.0" "1.14.1" "1.4.0" "1.14.0" >>>>> >>>>> Thanks, >>>>> Markus >>>>> >>> >>> >> > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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
ADD REPLYlink written 11.0 years ago by James W. MacDonald47k
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