[BioC] Sliding window t-test?

[Julian Gehring]

Hi Tim,

the 'les' (Loci of Enhanced Significance) package could be suited for
your analysis.

In a first step you assess the effect between the groups for each probe
with a statistical test (as you have already done with the t-test, but
you could also use other tests). Then, the les package estimates the
degree of significant probes within a sliding window along the genome.
This is based on a non-parametric estimation of the distribution of the
p-values, and hence you do not have to specify a threshold or correct
for multiple testing. Finally, you can search for regions with a high
degree of significant probes which would correspond to methylated
regions.

We have successfully used this to analyze methylation arrays while in
principle it is suited for all kinds of tiling arrays.

Another package applying a sliding window approach is 'rMAT', but
it seems to be specific for Affymetrix tiling arrays.


Best
Julian