[BioC] FC calculation in Limma

[Simon Anders]

Hi Lana

 > On Tue, Jan 18, 2011 at 9:20 PM, Lana Schaffer<schaffer at scripps.edu> 
  wrote:
 >> Kasper,
 >> How do you tell customers that the fold-change is not the
 >> Average of X divided by the average Y signal?

On 01/19/2011 04:32 AM, Kasper Daniel Hansen wrote:
> If they are savvy I would explain that the log scale is the relevant
> scale for analysis of microarrays and that they should therefore start
> by log transforming.  A corollary to this is (of course) that fold
> changes are calculated as they are.  I would explain that this has to
> do with the distribution of noise in the intensity measurements.
>
> If they are less savvy I would make an authoritative argument and
> would say that this is how it has been done in the field in the last
> 10 years or more.
>
> If this does not help, I would count myself lucky that they are not my
> collaborators.  Of course, that does not help you.


And if you want to sidestep the argument by giving your customers 
another way of looking at it, you might say: "Of course, the fold change 
is the average of X divided by the average of Y, but it is important to 
use the geometric, not the arithmetic average."

If you put it this way, the question is what averaging method to use, 
not what scale to average on. Of course, this is mathematically 
equivalent (the log of the geometric mean is equal to the arithmetic 
mean of the logs), but maybe more palpable to people who are scared of 
logarithms.

Have fun with your customers ;-)

   Simon