[BioC] RNAseq machine learning classifier

[Michael Love]

On Thu, Jul 18, 2013 at 4:45 PM,  <jhua at tgen.org> wrote:
> Hi, Mike:
>
> My approach is the same as Simon Anders's.
>
> For our data, the variance is low in low counts region.  The variance increases with counts, yet somehow start to dip suddenly at very high counts region.
>
> Do you have any experience with such type of data?  Is this normal?
>

This sounds somewhat like a description of the meanSdPlot for the
log2(n + 1) transformation in the vignette (or are you referring to
the VST data?).  We do see an increase then decrease of variance/sd of
log transformed data, though the location of the turning points will
obviously depend a lot on the experiment and on the range of the mean
counts.  Therefore a good argument for using VST.

Mike