[BioC] loess and limma

[Sean Davis]

On Thursday 14 September 2006 08:46, you wrote:
> Hi Sean
>
> Thanks for the reply. I guess what you are confirming that it is because
> there are too few points. I guess what surprised me was that there was
> absolutely no trace of a result. Have you any idea how many points are
> needed for the data to become "real"?

John,

Loess assumes that there is supposed to be no correlation between average 
intensity and ratio--that is why it works.  What you did with your experiment 
was to create a situation where there was a strong correlation between ratio 
and average intensity, thus violating that assumption.  If that assumption is 
wrong, as it is for your data, loess will still do the calculations, but it 
will remove that correlation, which in your case represents signal.  

So, "real" data doesn't relate to the number of points, it means that the 
assumption of no correlation between ratio and average intensity holds, which 
I have generally found to be the case for gene expression data, at least to a 
working approximation.  If that assumption DOES NOT hold, as in your data and 
array CGH, loess is not the correct method for normalization.

Hope that helps.
Sean