Entering edit mode
Ramon Diaz
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1.1k
@ramon-diaz-159
Last seen 10.3 years ago
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.
--
Ram?n D?az-Uriarte
Centro Nacional de Investigaciones Oncol?gicas (CNIO)
(Spanish National Cancer Center)
Melchor Fern?ndez 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)
**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en
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