[BioC] limma background correction

[Henrique Proença]

Dear Gordon,

I have tried the 2.15.10 version of limma with R 2.8.0 and it works fine 
for the data set that previously gave errors.
Thanks a lot for your help.

Regards
Henrique Proença
--------------------------


Gordon K Smyth 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
> 
> _______________________________________________
> Bioconductor mailing list
> 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
>