[BioC] Problems reading single channel GenePix data with read.maimages.

[Paul Geeleher]

Hey Everyone,

I'm having a problem reading some single channel GenePix data.

I use the following code to read the files:

# define column names
Cy3 <- "F543 Median"
Cy3b <- "B543 Mean"

# read targets and load data, the current directory contains the .gpr files
library("limma")
targets <- dir()
RG <- read.maimages( targets,
source='genepix',columns=list(R=Cy3,G=Cy3, Rb=Cy3b, Gb=Cy3b))


Now I'm using exactly the same code for two different single channel
GenePix datasets, one works fine, the other throws this error after
trying to read the images (the last line above):

"""
Error in read.table(file = file, header = TRUE, col.names = allcnames,  :
duplicate 'row.names' are not allowed
"""

I'm not sure what its referring to as both files have duplicate gene
names (which I presume are row names?). I've uploaded some samples of
files from either dataset:

http://frink.nuigalway.ie/~pat/works.gpr
http://frink.nuigalway.ie/~pat/doesntWork.gpr


One more difference is that the files that don't work have a separate
GAL file. I don't know if this makes a difference.

Thanks for any help folks.




> sessionInfo()
R version 2.8.1 (2008-12-22)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_IE.UTF-8;LC_NUMERIC=C;LC_TIME=en_IE.UTF-8;LC_COLLATE=en_IE.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_IE.UTF-8;LC_PAPER=en_IE.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_IE.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_2.16.4


-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland