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Question: Problem with read.maimages (Limma): Error in dimnames(x) <- dn
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gravatar for Hari Easwaran
6.7 years ago by
Hari Easwaran230
United States
Hari Easwaran230 wrote:
Hi Axel, Thanks for pointing out the error in the way I was specifying the "names" field (names= targets[,"Names"]). My targets file actually has 8 rows (8 files). Initially I had some other problem reading them (there was an error in the file names), so I started working with only one file. But I was not careful enough during copy-pasting and pasted names= targets[,"Names"] instead of names= targets[1,"Names"]. The latter error ran me into the problem I reported. Thanks for pointing that. Now the I can load the files without issues. BTW, I double checked the Agilent file and the version I have has a column "GeneName". This data was generated last week. May be it is a version issue. Again, thanks Axel and Martin. Best, Hari On Mon, Mar 7, 2011 at 11:11 AM, <axel.klenk@actelion.com> wrote: > Dear Hari, > > without knowing your targets data.frame and your input file(s) > I can only offer some wild guessing... > > Guess #1, since the error message complains about a mismatch of dimnames > [2], > ie. column names: you are reading a single file "filename.txt" and set > column names > to targets[,"Names'] -- is there really only one row in your targets? And > if you have a > targets dataframe, why not use it as an argument to read.maimages() as > shown in > the limma user's guide? > > Guess #2, the 8x60K data files I have for testing do not contain a column > "GeneName" > which is probably due to different Agilent FES output file formats... can > you make sure, > your files do have that column? > > BTW, when reading Agilent files with read.table() and friends, you'll have > better results > using argument "skip = 9" instead of "fill = T"... > > Hope this helps, > > - axel > > > Axel Klenk > Research Informatician > Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / > Switzerland > > > > > From: > Hari Easwaran <hariharan.pe@gmail.com> > To: > <bioconductor@stat.math.ethz.ch> > Date: > 07.03.2011 16:23 > Subject: > [BioC] Problem with read.maimages (Limma): Error in dimnames(x) <- dn > Sent by: > bioconductor-bounces@r-project.org > > > > Dear all, > I apologize for resending the following mail that I had sent last week. > Usually the bioconductor group is so quick in providing solutions, I am > wondering if my mail didn't go through. Please excuse if you have already > seen this. > > I am encountering the following error with read.maimages in limma package. > Error in dimnames(x) <- dn : > length of 'dimnames' [2] not equal to array extent > > Following are some details: > Here is the command I am using: > read.maimages("filename.txt", source="agilent", > columns=list(G="gMedianSignal", Gb="gBGMedianSignal", R="rMedianSignal", > Rb="rBGMedianSignal"), names= targets[,"Names"], annotation = c("Row", > "Col","FeatureNum", "ControlType","ProbeName", "GeneName")) > > I am trying to open Agilent 8x60K data. Previously I have worked > with Agilent 44K data without any issues. I tried to open the file using > read.table with the following command which works: > > x <- read.table("filename.txt", sep="\t",fill=T) > Without the "fill=T" option, I get an error that "line 1 did not have 205 > elements". I wonder if read.maimages is not able to read the file because > all columns do not have some values (I mean some character in it). > However, > I am not an R expert, and so dare not speculate too much. I tried passing > "fill=T" to read.maimages, but got the following error: > Error in read.columns(fullname, required.col, text.to.search, skip = skip, > : > formal argument "fill" matched by multiple actual arguments > > I searched the web for solutions but couldn't find any. Some of the > suggestions I found was to update limma version. However, in my case, I > had > re-installed limma again today. > > My session info: > R version 2.12.1 (2010-12-16) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] limma_3.6.9 > > loaded via a namespace (and not attached): > [1] tools_2.12.1 > > > > Any help is greatly appreciated. > > Sincerely, > Hari Easwaran > Johns Hopkins University > Baltimore, MD > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > The information of this email and in any file transmitted with it is > strictly confidential and may be legally privileged. > It is intended solely for the addressee. If you are not the intended > recipient, any copying, distribution or any other use of this email is > prohibited and may be unlawful. In such case, you should please notify the > sender immediately and destroy this email. > The content of this email is not legally binding unless confirmed by > letter. > Any views expressed in this message are those of the individual sender, > except where the message states otherwise and the sender is authorised to > state them to be the views of the sender's company. For further information > about Actelion please see our website at http://www.actelion.com > > [[alternative HTML version deleted]]
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