[BioC] illumina --> limma?

[Wolfgang Huber]

Hi Axel,

> Maybe it is to mention that for some normalisations, the log-values can 
> get negative (i.e. for expression values lower than 1). To proceed you 
> can convert the negative values to the smallest positive value. So add 
> this line:
> 
> exprs(newExprSet)[ exprs(newExprSet) < 0 ] = min(exprs(newExprSet)[ 
> exprs(newExprSet) > 0 ])

But that is a really bad idea. There has been a lot of research into 
this, and if you use a decent normalization method you will not have 
this problem. Data transformation (e.g. log) and the preceding 
background correction step have to be considered together, and depending 
on your taste, you can either use a method that

1. biases the background correction in such a manner that the values 
stay away well above zero, so that you then can safely apply the 
logarithm, or

2. use an unbiased background correction, but then apply a 
variance-stabilizing transformation function (glog) that is meaningful 
even with negative values.

There are many parallels between the two approaches, the bottom line 
results can be quite similar. The 'vsn' package offers software for doing 2.


  Best wishes
  Wolfgang