Hi Sylvain,
You can try calling the aqm.xxx functions separately (aqm.maplot,
aqm.boxplot, aqm.heatmap and so on), as described in the vignette and set up
the graphical parameters so that they suit better to your data size.
Best wishes,
Audrey

2010/4/28 Sylvain Foisy <sylvain.foisy@diploide.net>

> Hi,
>
> I usually use arrayQualityMetrics with less than 20-30 chips and never
> cared
> about the outputs until now. I have a 70 Affy chips study and although the
> graphs are useful, they are not really presentable: most of the axis legend
> and labels are really squashed, the typeface barely readable...
>
> I know it is probably a very newbie question but it is a new problem for
> me.
> What steps should I take to prettify the graphs? This is my usual
> procedure:
>
> >library(arrayQualityMetrics)
> >library(simpleaffy)
> >data<-read.affy(covdesc="covdesc")
> >arrayQualityMetrics(data,
> + outdir = getwd(),
> + intgroup = "Treatment",
> + grouprep = True,
> + spatial = FALSE)
>
> Thanks in advance
>
> Sylvain
>
>
> ===================================================================
>
>  Sylvain Foisy, Ph. D.
>  Consultant Bio-informatique / Bioinformatics
>  Diploide.net - TI pour la vie / IT for Life
>
>  Courriel: sylvain.foisy@diploide.net
>  Web: http://www.diploide.net
>  Tel: (514) 893-4363
>
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>



-- 
Audrey Kauffmann
Bergonie Cancer Institute
229 Cours de l'Argonne
33076 Bordeaux
France
+33.5.56.33.04.53

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