[BioC] Log transformation and left censoring

[Paul Harrison]

On Sun, Feb 3, 2013 at 10:24 PM, Wolfgang Huber <whuber at embl.de> wrote:
>
> Hi Paul
>
> given your description, one possibility to explore might be a variance
> stabilising transformation.
>
> E.g. DESeq provides one that smoothly interpolates between the square-root
> function for low counts and the log-transformation for higher counts, see
> Section 6 (and 7) of the vignette.
>

Thanks Wolfgang. Zero is tranformed to the same value in each of the
samples, which is good. The ability of limma to detect differential
expression with this transformation appears to be about the same as
with voom. But perhaps I should be using DESeq's nbinomTest.

I do wonder if this is still too mild near zero. When I plot variance
for each gene vs mean for each gene, there is a distinct bump at low
expression levels. Looking at vst.pdf the assumption seems to be that
the variance of a zero count is zero, which isn't correct. Seeing a
zero count, my expectation of the true mean would be somewhat greater
than zero, and so the variance would also be somewhat greater than
zero.

--
Paul Harrison

Victorian Bioinformatics Consortium / Monash University