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

[Ramon Diaz-Uriarte]

Dear John,

Thanks for your answer and checking it.

Best,

R.

On Friday 12 January 2007 10:39, J-C. Marioni wrote:
> Hi Ramon,
>
> Like you, I'm a little puzzled by this. mergeLevels.new
> should be the function Jane wrote. However, clearly something has gone
> wrong in our implementation or an old version of the code has been
> uploaded into BioConductor. While the functions (mergeLevels and
> mergeLevels.new) are clearly quite similar, there are differences. The
> fault is almost certainly with us and I will endeavour to sort out the
> problem ASAP.
>
> Thanks for pointing this out.
> John
>
> >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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