[BioC] Problem with read.maimages (Limma): Error in dimnames(x) <- dn

[Martin Morgan]

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]]
> 
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