Dear Simon,

At present any combination of 'transform' and 'method' are allowed.  The transformation is applied prior to the normalisation without any checking for whether the options are sensible.

As you point out, to use vsn you will need transform="none" and method="vsn" (other options will lead to a log2 or vst transform being applied prior to vsn).

I will add some checks to normaliseIllumina() to ensure that only sensible options are allowed in future.

Best wishes,

Matt

-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Simon Anders
Sent: Fri 2/1/2008 2:06 PM
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] beadarray / normaliseIllumina and logarithm
 
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
| office phone +44-1223-494478, mobile phone +44-7942-583830
| preferred (permanent) e-mail: sanders@fs.tum.de

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