Thanks Gordon - a very helpful response and reference.

(In future I shall endeavour use 'raw' for untransformed rather than
'linear' which is the way I always thought about the non-log scale on the
other face of my old slide rule)


On Fri, Feb 17, 2012 at 8:54 AM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> Dear Ross,
>
> Short answer:
>
> The vst transformation is asymptotically equivalent to the log2, and
> 2^logFC is the correct transformation.
>
> Longer answer:
>
> See
>
>  http://www.ncbi.nlm.nih.gov/**pubmed/20929874<http://www.ncbi.nlm.nih.gov/pubmed/20929874>
>
> for why vst gives small fold changes, and what you should do about it.
>
> BTW, there is nothing "linear" about raw scale intensities for
> fold-changes.  The logFC are far more linear in their statistical behaviour.
>
> Best wishes
> Gordon
>
>  Date: Thu, 16 Feb 2012 14:58:02 +1100
>> From: Ross <ross.lazarus@gmail.com>
>> To: bioconductor@r-project.org
>> Subject: [BioC] Estimating fold change from limma 'log2FC' using lumi
>>        vst instead of log2 transformation?
>>
>> Dear Bioconductors,
>>
>> I have a question related to estimates of microarray expression fold
>> change
>> after using vst in lumi (as the authors recommend) rather than a simple
>> log2 transformation. I apologise if this is a foolish question or if my
>> google-fu was too weak to find the answer when I searched.
>>
>> I am working with illumina sentrix expression data, using lumi's vst and
>> quantile normalization, then limma to model differential expression.
>>
>> One of my collaborators has asked for the fold changes reported by limma
>> (as log2FC) on a linear scale so he can check the top ones with qPCR.
>>
>> Initially, I was going to make the obvious suggest that he take 2^log2FC
>> to
>> transform what lumi reported as log2FC back to a linear scale - but this
>> probably not the right transformation - because vst is not log2!
>>
>> To confirm this, I reran the analysis replacing the lumi vst option with a
>> log2 transformation to see what differences there were.
>> ...stuff deleted for brevity
>
>

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