On Tue, Feb 28, 2012 at 8:21 AM, Olivier Grisel <[email protected]> wrote: > 2012/2/28 Brent Pedersen <[email protected]>: >> Hi, >> is there an example in the docs that I'm missing of using >> PCA to remove batch effects? > > I don't really know what you mean by batch effects but I assumes you > want to get rid of low frequency components in images or sounds or > noisy generic topics (such as generic stop words) in text documents. >
In this case, I am looking at microarray data. Batches done on different dates or in different labs tend to cluster together. >> If I understand correctly, I may be able to do this by >> using U, S, V = pca._fit(X) and then removing the first n_components. >> Is there a way to do this so I can then use inverse_transform >> to get the data in the original projection with batch effects >> removed? > > I think you should write your own class that derives from sklearn PCA > or RandomizedPCA and implement transform and inverse_transform as you > wish. > I will look into this. Thanks. > -- > Olivier > http://twitter.com/ogrisel - http://github.com/ogrisel > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Scikit-learn-general mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/scikit-learn-general ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ Scikit-learn-general mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/scikit-learn-general
