[BioC] Duplicate row.names error
Jean Yee Hwa Yang
jeany at maths.usyd.edu.au
Mon Jun 26 23:05:31 CEST 2006
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.
Can you send me off-list the output for pigTargets.
On Mon, 26 Jun 2006, Andre wrote:
> 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:
> 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.
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