[BioC] RNAseq machine learning classifier

[jhua at tgen.org]

Hi, Mike:

Actually both log2(n+1) and VST gives roughly the same meanSdPlot, although VST one is slightly flatten.

Jianping



On Jul 19, 2013, at 2:35 AM, Michael Love wrote:

> 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