[BioC] Duplicate row.names error

Jean Yee Hwa Yang jeany at maths.usyd.edu.au
Mon Jun 26 23:05:31 CEST 2006

Hi Andre,

Currently read.Galfile uses "ID" as the unique rownames.  We assume that 
ID contains information such as probe ID whereas the column "Names" can 
contain duplicate gene names.  However, I don't think that should stop you 
from reading in the gpr file.  If you have those two columns swap in your 
gal file you might want to try:

read.Galfile("XXXX", info.id = c("Name", "ID"), labels = "Name")
where XXX is the name of any of your gpr file or your gal file.

In addition, 
Can you send me off-list the output for pigTargets.



On Mon, 26 Jun 2006, Andre wrote:

> Hello,
> I am new to the marray package and I am using it to read .GPR files. Here is
> the sequence of commands that I entered and the resulting error:
>> library(marray)
> Loading required package: limma
>> datadir <- "P:/Manually flagged"
>> pigTargets <- read.marrayInfo(file.path(datadir, "JG2.7 target file.txt"))
>> mraw <- read.GenePix(targets=pigTargets, path = datadir)
> Error in "row.names<-.data.frame"(`*tmp*`, value = c("1", "1", "1", "1",  :
>        duplicate 'row.names' are not allowed
> Our microarray data includes duplicated genes and therefore, duplicated gene
> names and this could be what is causing the error. Is there anyway to
> bypass/fix this?
> Thanks for your help.
> Andre
> 	[[alternative HTML version deleted]]
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