Hi,

sorry, there is currently nothing in aroma.affymetrix for calling
probes present/absent.  For questions on affy::mas5calls(), check with
the Bioconductor mailing list.

Cheers,

Henrik

On Tue, Sep 25, 2012 at 4:05 PM, Heather Wick <heather.c.w...@gmail.com> wrote:
> I would like to look at present/absent calls and the associated p-values for
> a set of MoGene ST arrays I'm working on. I normalized the chips using the
> Aroma vignette, but there are no instructions there for P/M/A calls.
> Normally, I work with Hgu133plus2 arrays, so my instinct was to try reading
> the cel files in with ReadAffy and then using mas5calls to extract this
> data. However, I got this error:
>> data.mas5calls=mas5calls(CelData)
> Getting probe level data...
> Computing p-values
> Error in FUN(1:11[[1L]], ...) :
>   NA/NaN/Inf in foreign function call (arg 2)
>
> I'm sure there must be a way of getting present/absent calls/pvalues with ST
> arrays, can someone point me in the right direction?
>
> I was also disappointed that I could not get percent present, average
> background, or scale factor using qc on these chips; is there an equivalent
> function for ST arrays?
>
> I cannot seem to find any information about this on the Aroma website or
> searching through the forums. I greatly appreciate any advice you can offer.
> ~ Heather Wick
>
> --
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version of the package, 2) to report the output of sessionInfo() and 
traceback(), and 3) to post a complete code example.


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