[BioC] limma background correction

Ulrike Goebel ugoebel at mpiz-koeln.mpg.de
Thu Jul 10 17:35:51 CEST 2008

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 !


On Thursday 10 July 2008 17:13, Henrique Proença 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
  +49(0) 221 5062 121

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