[BioC] limma background correction

[Gordon K Smyth]

Hi Artur,

R 2.8.0 is available pre-compiled for Windows, so you can install it 
anytime as you did with R 2.7.X.  The current version is available from 
the University of North Carolina:

http://mirrors.ibiblio.org/pub/mirrors/CRAN/bin/windows/base/R-2.8.0dev-win32.exe

or from

http://cran.at.r-project.org/bin/windows/base/R-2.8.0dev-win32.exe

Best wishes
Gordon

On Wed, 27 Aug 2008, Artur Veloso wrote:

> Dear Gordon and all,
>
> I am having the same problem that Ulrike and Henrique were, but I don't know
> how to compile R for my Windows PC. Is there a somewhat easy way to do this
> or should I put these analyses on the back burner and wait for R 2.8.0 to be
> released?
>
> I appreciate any advice,
>
> Artur Veloso
> Hollings Marine Laboratory
> 331 Fort Johnson Road
> Charleston, SC, 29412, USA
>
> On Fri, Jul 11, 2008 at 10:14 PM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>
>> Dear Ulrike and Henrique,
>>
>> The problem is more likely to be with the limma normexp.fit() function than
>> with optim().
>>
>> There is a rare numerical instability which causes an error like this with
>> normexp background correction in limma 2.14.X.  Jeremy Silver and I did a
>> lot of work on this late last year, and we think we have eliminated the
>> problem.  The new (faster) code is in limma on the Bioconductor
>> developmental repository.  You can try it out if you install R 2.8.0.  I'd
>> be interested to know if it solves the problem for your data sets.
>>
>> Best wishes
>> Gordon
>>
>>  Date: Thu, 10 Jul 2008 17:35:51 +0200
>>> From: Ulrike Goebel <ugoebel at mpiz-koeln.mpg.de>
>>> Subject: Re: [BioC] limma background correction
>>> To: bioconductor at stat.math.ethz.ch
>>> Message-ID: <200807101735.52255.ugoebel at mpiz-koeln.mpg.de>
>>> Content-Type: text/plain;  charset="iso-8859-1"
>>>
>>> Hi Henrique,
>>>
>>> I recently got the same error with a Nimblegen dataset. Because in this
>>> dataset the background is actually not provided (the corresponding column
>>> is
>>> all-zero), I figured that was the reason ... However, this error occurs
>>> only
>>> with R-2.7.0, not with 2.6 or 2.5. So something must have changed in the
>>> optim() function (this is where it crashes in my case).
>>>
>>> Glad to hear that I am not the only one who stumbled across this !
>>>
>>> Ulrike
>>>
>>> On Thursday 10 July 2008 17:13, Henrique Proen?a wrote:
>>>
>>>> Hi,
>>>>
>>>> I am trying to analyze some quantarray files using limma Guide, when
>>>> suddenly it gives me the following error at the background normalization
>>>> step (using normexp method and offset = 50)
>>>>
>>>> Error in if (all(abs(delta) < 1e-10)) break :
>>>>   missing value where TRUE/FALSE needed
>>>>
>>>> I can't find why this happens.
>>>> Does anyone an idea of what is happening?
>>>>
>>>
>>> --
>>>  Dr. Ulrike Goebel
>>>  Bioinformatics Support
>>>  Max-Planck Institute for Plant Breeding Research
>>>  Carl-von-Linne Weg 10
>>>  50829 Cologne
>>>  Germany
>>>  +49(0) 221 5062 121
>>>
>>
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>