[BioC] beadarray / normaliseIllumina and logarithm

[Simon Anders]

Hi,

I am a bit unsure whether I have correctly understood the help page of
normaliseIllumina (of package beadarray) with regards to the question
when this function logarithmizes the expression data.

The help page says:

  Note: If your 'BSData' object contains data already on the
      log-scale, be careful that you choose an appropriate 'transform'
      to avoid logging it twice.  The same applies for the '"vst"'
      transformation and '"vsn"' normalisation methods which require the
      expression data stored in 'BSData' to be on the original
      (un-logged) scale.

Does with mean that a transformation to log scale (via log or glog)
happens _only_ when 'transform' is 'log2' or 'vst' or 'method' is 'vsn'?

Does it mean furthermore that for 'method="vsn"', 'transform' _must_ be
set to 'none' to avoid double logarithmizing?


Thanks
   Simon



+---
| Dr. Simon Anders, Dipl.-Phys.
| European Bioinformatics Institute, Hinxton/Cambridge, UK
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