Re: [pymvpa] effect size (in lieu of zscore)

2012-01-06 Thread Mike E. Klein 
Hi all,

Thanks again for the continued help. I think the skews are for the reasons
suggested here… I'm seeing them in a couple subjects in the positive
direction as well as the negative, and I've made quite certain that my
preprocessing is correct. I'll be mindful of the histos and, for now,
continue on with analyses!

Best and thanks again,
Mike

On Wed, Jan 4, 2012 at 6:13 PM, Francisco Pereira 
francisco.pere...@gmail.com wrote:

 On Wed, Jan 4, 2012 at 6:04 PM, J.A. Etzel jet...@artsci.wustl.edu
 wrote:
 
  Non-independence is definitely a big issue (not the only one,
 unfortunately).

 It's most definitely an issue. Michael Hanke helped me think about
 this and we tried to suggest one possibility for testing for the
 presence of that in page 7 of
 http://www.princeton.edu/~fpereira/Papers/searchmight.pdf
 (pardon the self reference)

 There will be code to help diagnose this in the next version of
 Searchmight. That said, I think that this is more of a problem in
 terms of making results that are marginal appear significant, rather
 than introducing bias one way or another.

  doesn't seem unusual to have a few subjects with below-chance
 classification
  in large numbers of voxels; I don't think the current methods deal with
 this (or even explain it) very well.

 Right, with a large number of voxels where the underlying accuracy is
 at chance level a fraction of will them will appear much worse than
 chance, just as a fraction will appear much better than chance. With
 enough subjects...

 Francisco

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[pymvpa] Saving trained classifiers

2012-01-06 Thread Tyson Aflalo 
Is there a method to save trained classifiers and other non-dataset
datatypes?
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Re: [pymvpa] Saving trained classifiers

2012-01-06 Thread Yaroslav Halchenko 
unfortunately only some.  E.g. we have not implemented yet storing of
classifiers which are interfaced into Python via swig'ed backends, such
as SVMs.  Otherwise, classifiers, as other structures (datasets,
mappers, etc) should be storable in mvpa2 the same way as datasets using
h5save, h5load functions.  Here is the corresponding unittest:

https://github.com/PyMVPA/PyMVPA/blob/HEAD/mvpa2/tests/test_hdf5_clf.py#L78

On Fri, 06 Jan 2012, Tyson Aflalo wrote:

Is there a method to save trained classifiers and other non-dataset
datatypes? �

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