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

[Pan Du]

The "seed" is a function parameter. Users can easily change it. Thanks.


Pan 


On 5/8/08 12:41 PM, "Kasper Daniel Hansen" <khansen at stat.Berkeley.EDU>
wrote:

> Please don't put seed inside functions, it may mess up the random
> number stream. If someone wants reproducible plots you should either
> increase the number of points are let him set the seed himself.
> 
> Kasper
> 
> On May 8, 2008, at 7:35 AM, Pan Du wrote:
> 
>> 
>> 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,
>> 
>> 
>> Pan
>> 
>> 
>> 
>> 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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>>>> Search the archives:
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>>> 
>>> -- 
>>> Dr. Matthias Kohl
>>> www.stamats.de
>>> 
>> 
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>