[BioC] Pairs plots in lumi, plots look different?

Matthias Kohl Matthias.Kohl at stamats.de
Wed May 7 12:41:48 CEST 2008


the default pairs plot uses a random subset of the data

pairs(x, ..., logMode = TRUE, subset = 5000)


Hence, each call of pairs leads to different results. By setting the 
random seed or the argument "subset" appropriately you could obtain 
identical plots for each call.

Best regards,

Julien Bauer wrote:
> Hello,
> I am working for a microarray facility at Cambridge University, we 
> have been using the Illumina platform for a while now.
> Lumi is a great package but I noticed something rather odd, when using 
> the plot function "pairs" on my data, if I run it again the plots look 
> different, some points are shifted or change location. The rest stay 
> the same it just the look of the graphs that change.
> My guess is that it is because of the auto scaling of the graph but I 
> would like to be sure. I look in the mailing list archive and in the 
> vignette but I couldn't find the answer for this.
> Thanks in advance for your help,
> Julien Bauer
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Dr. Matthias Kohl

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