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. -- 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 s...{{dropped}}