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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