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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:
Dear all, 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("jhu_252800413205_S01_GE2_107_Sep09_1_1_JL8-Cy3_JL7-Cy 5.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]]
ADD COMMENTlink modified 6.7 years ago • written 6.7 years ago by Hari Easwaran230
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gravatar for Hari Easwaran
6.7 years ago by
Hari Easwaran230
United States
Hari Easwaran230 wrote:
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]]
ADD COMMENTlink written 6.7 years ago by Hari Easwaran230
On 03/07/2011 07:22 AM, Hari Easwaran wrote: > 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 I'd guess this was a locale issue; see ?Sys.locale and using locale="C". Also I went http://bioconductor.org/help/mailing-list/ and searched for "read.maimages 2011" to find https://stat.ethz.ch/pipermail/bioconductor/2011-February/038017.html which might also be relevant. Martin > > 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD REPLYlink written 6.7 years ago by Martin Morgan ♦♦ 20k
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 at="" gmail.com=""> To: <bioconductor at="" 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 at 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 at 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
ADD REPLYlink written 6.7 years ago by Axel Klenk820
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