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@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@mpiz-koeln.mpg.de>
>> Subject: Re: [BioC] limma background correction
>> To: bioconductor@stat.math.ethz.ch
>> Message-ID: <200807101735.52255.ugoebel@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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