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

[axel.klenk at actelion.com]

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

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