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

Pan Du dupan at northwestern.edu
Thu May 8 16:35:22 CEST 2008

Yes, as Matthias mentioned, we use random subset to increase the efficiency
of plotting. To avoid variations over different plots, I have added the
"seed" parameter to the these plot functions. Please check the latest
developing version of lumi 1.7.3. Thanks for using lumi!

Best regards,


On 5/8/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 1
> Date: Wed, 07 May 2008 12:41:48 +0200
> From: Matthias Kohl <Matthias.Kohl at stamats.de>
> Subject: Re: [BioC] Pairs plots in lumi, plots look different?
> To: Julien Bauer <jb393 at cam.ac.uk>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID: <4821876C.3020705 at stamats.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Hello,
> the default pairs plot uses a random subset of the data
> pairs(x, ..., logMode = TRUE, subset = 5000)
> confer
> library(lumi)
> ?"pairs-methods"
> 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,
> Matthias
> 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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>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> -- 
> Dr. Matthias Kohl
> www.stamats.de

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