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

[Martin Morgan]

Paul Geeleher <paulgeeleher at gmail.com> writes:

> 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"

I don't think these are column headers in works.gpr...

> # 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 think the problem here is that a friendly piece of software has
added tabs after the last field of each data record (and changed the
encoding of file column names -- look after some of the Rgn R
columns). I think you can get away with adding row.names=NULL to
read.maimages but I'd check carefully that you've pulled in the right
columns.

Martin

> 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

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793