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
>
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