[BioC] mergeLevels (aCGH) vs. MergeLevels.new

[Ramon Diaz-Uriarte]

Dear All,

I am confussed about the differences between mergeLevels (in package aCGH) and 
MergeLevels.new (package snapCGH), and which one is the recommended merging 
procedure to use.

By the description in the help, mergeLevels (aCGH) is the one used in the 
Willenbrock & Fridlyand Bioinformatics 2005 paper. The defaults of 
mergeLevels (Wilcoxon p-value, Ansari p-value, etc) are also those used in 
the Bioinformatics paper. And the Bioinformatics paper is cited in the help.

MergeLevels.new (snapCGH)  is the function called by mergeStates (also in 
package snapCGH) when MergeType = 1.  I think MergeLevels.new is clearly NOT 
doing what is described in the Bioinformatics paper: that paper is not cited 
in the help, the defaults of the algorithm are different, and even the 
workings of the algorithm seem to differ. 

I am confussed, because from the help of mergeStates that says "1 uses a new 
merging algorithm  developed by Hanni Willenbrock and Jane Fridlyand.", it 
would seem that MergeLevels.new is the recommended way to go. But option 2 
(i.e., MergeLevels.old) is not the same as mergeLevels from aCGH either (it 
seems to be the former merging algorithm in the JMVA paper by Fridlyand et 
al.).

So, there are three algorithms, mergeLevels (aCGH), MergeLevels.new (snapCGH) 
and MergeLevels.old (snapCGH). Among the first two, which one should be used? 
And, if MergeLevels.new is the currently recommended one, are there any 
references?



Thanks,

R.

-- 
Ramón Díaz-Uriarte
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)



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