Hi Mario.
I will look into this. I know this feature doesn't get used too often
for these new arrays. As you may know, it will need to be called
differently than when using it for 3' IVT arrays (e.g. HG-U133).
Can you give me your sequence of commands? I assume you have
specified the set of negative control indices to use, right?
Cheers,
Mark
On 24/03/2009, at 8:57 PM, Mario Fasold wrote:
>
> Hi all! I'd like to use gcRMA correction on Human Gene 1.0 ST data.
> However, the method GcRmaBackgroundCorrection fails, probably since
> the probe_tab file has a slightly different layout for these chips
> (see error message below). Is there a way of telling the gcRMA
> function to use different columns of the probe_tab file?
>
> Best, Mario.
>
> Reading tab-delimited sequence file...
> Error in if (any(units < 1)) stop("Argument 'units' contains non-
> positive indices.") :
> missing value where TRUE/FALSE needed
>
> >
------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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