Thanks a lot for your comments. I did try earlier on to remove the bad points but came across some problems when re-ordering my array. I will try out the method sent to me and check the reference.
<kgdunn+nabble@...287...> 02/11/09 4:06 PM >>>
I am assuming your masked array entries are missing data. Multivariate analysis with missing data can be handled in several standard ways, however these methods don't appear in most Python libraries.
Here are some references on the topic that will help you:
 P.R.C. Nelson and J.F. MacGregor, 1996, "Missing data methods in PCA and PLS: Score calculations with incomplete observations", Chemometrics and Intelligent Laboratory Systems, v35, p 45-65.
 F. Arteaga and A. Ferrer, 2002, "Dealing with missing data in MSPC: several methods, different interpretations, some examples", Journal of Chemometrics, v16, p408-418.
Paper  deals with building a model with missing data, while paper  looks at applying an existing PCA model to new data that contains missing entries.
Hope these help,
Marjolaine Rouault wrote:
I am struggling to do a PCA analysis on a masked array. Anybody has
suggestions on how to deal with masked array when doing PCAs?
Best regards, Marjolaine.
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