Using traceback give the following: > traceback() 5: stop("row names supplied are of the wrong length") 4: data.frame(sample = 1:length(sampleNames), row.names = sampleNames) 3: read.phenoData(sampleNames = colnames(signal), widget = FALSE) 2: readBead(datafile, version = "Two") 1: beadAnalysis() It can be run without the widget by instead using: >Data<-readBead("Sample_Probe_Profile.csv") Looking at this I think the "wrong length" error, when using the txt file is coming from the "skip" argument in the read command as the txt file from version 2 has no header rows to skip. The version "One" reads the csv format.. But trying this I then get an error > data<-readBead("Sample_Probe_Profile.csv",version="One") Read Sample_Probe_Profile.csv Error in read.table(file = file, header = header, sep = sep, quote = quote, : duplicate 'row.names' are not allowed Enter a frame number, or 0 to exit 1: readBead("Sample_Probe_Profile.csv", version = "One") 2: read.delim(filenames[1], skip = 7, sep = ",", row.names = 1) 3: read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, comment.char = comment.cha But my data comes from a Illumina Inc. BeadStudio version 2.3.41 so this doesn't seem like the right way to go about it. Does the row.names=1 refer to the first column? As there are a few target Ids (the first column) that have two probes so more than one row.. -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Thursday, 18 October 2007 5:32 p.m. To: Johnstone, Alice Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] BeadExplorer error Hi Alice -- It's a pretty good error! how can row.names(x) have a length different from 1:length(x)? The answer is... > x <- character(0) > data.frame(1:length(x), row.names=x) Error in data.frame(1:length(x), row.names = x) : row names supplied are of the wrong length because length(x) is 0 and 1:0 is c(1,0). So my guess is that the sample names are not being read correctly from Sample_Probe_Profile.csv. The use of widgets makes it difficult to track down further or make a reproducible example, though traceback() (and options(error=recover), for the enthusiastic) might be helpful. Does that point in the right direction? Martin "Johnstone, Alice" <alice.johnstone at="" esr.cri.nz=""> writes: > Hi > I have been trying to get BeadExplorer to work with my Illumina data, > but I get the following error when using either the txt or csv files: > >> data<-beadAnalysis() > Read c:/R/Illumina/Sample_Probe_Profile.csv > Error in data.frame(sample = 1:length(sampleNames), row.names = > sampleNames) : > row names supplied are of the wrong length In addition: Warning > message: > read.phenoData is deprecated, use read.AnnotatedDataFrame instead > > > I do note that this error has been posted on here before, but I > haven't seen a resolution for it, can anyone help me here? > > Cheers, > Alice > >> sessionInfo() > R version 2.6.0 (2007-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New > Zealand.1252;LC_MONETARY=English_New > Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252 > > attached base packages: > [1] tcltk tools stats graphics grDevices utils datasets > > [8] methods base > > other attached packages: > [1] BeadExplorer_1.4.0 tkWidgets_1.16.0 DynDoc_1.16.0 > [4] R2HTML_1.58 widgetTools_1.14.0 limma_2.12.0 > [7] lumiRatV1_1.3.1 lumi_1.4.0 annotate_1.16.0 > [10] xtable_1.5-2 AnnotationDbi_1.0.5 RSQLite_0.6-3 > [13] DBI_0.2-4 mgcv_1.3-28 affy_1.16.0 > [16] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 > > > > > > > P Think before you print > This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed. > If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you. > > _______________________________________________ > 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 -- Martin Morgan Computational Biology Shared Resource Director Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (208) 667-2793