Re: [aroma.affymetrix] Multiple NUSE and RLE Plots?

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Re: [aroma.affymetrix] Multiple NUSE and RLE Plots?

Henrik Bengtsson
Hi,

On Fri, Sep 24, 2010 at 1:27 PM, Vonn <[hidden email]> wrote:

> Hi All,
>
> I'm using aroma to analyze CEL files from 141 SNP 6.0 arrays.  I fit
> the quality assessment model as follows:
>
> plm = RmaPlm(csR)
> fit(plm, verbose = log)
> qam = QualityAssessmentModel(plm)
>
> Then I'd like to produce NUSE and RLE plots for 10 arrays at a time.
> Can someone please tell me how to do this?

plotNuse() and plotRle() for QualityAssessmentModel takes argument
'arrays', e.g.

plotNuse(qam, arrays=1:10);
plotNuse(qam, arrays=11:20);
...

Note that the NUSE and RLE estimates are, as wanted, calculated using
the complete data set, that is, the 'arrays' argument is only applied
to the plotting part.

/Henrik

>
> Thanks in advance for your response,
>
> Vonn
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> 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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--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest 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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