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

[Wolfgang Huber]

Dear Pan,

as another option, you could explore the "smoothScatter" function from 
the "geneplotter" package. The examples in its manual page show how to 
use it as a panel function for "pairs".

Best wishes
   Wolfgang

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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


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

Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber