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List:       bioconductor
Subject:    Re: [BioC] Duplicate row.names error
From:       Jean Yee Hwa Yang <jeany () maths ! usyd ! edu ! au>
Date:       2006-06-26 21:05:31
Message-ID: Pine.LNX.4.63.0606270657340.23396 () pisa ! maths ! usyd ! edu ! au
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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:

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.

Cheers

Jean

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
>
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