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