[Ifeffit] Determining the correct number of components from PCA

Voegelin, Andreas Andreas.Voegelin at eawag.ch
Thu Aug 27 16:12:12 CDT 2009

Hi Kevin

Maybe the 3rd component is not due to noise but accounts for very small
shifts in energy calibration between scans (considering that the
reconstructed white-line is shifted to higher energies in the
2-component reconstruction). Do you have a reference foil measured with
each scan to exactly align the spectra or some other way to check for
small shifts in energy calibration?

Best regards,


-----Original Message-----
From: ifeffit-bounces at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Kevin
Sent: Donnerstag, 27. August 2009 07:23
To: ifeffit at millenia.cars.aps.anl.gov
Subject: [Ifeffit] Determining the correct number of components from PCA

Hi all,

I have a question about the "best" method to use to decide the correct
number of components in a system based on a PCA.  Myself and a
collaborator took in-situ XANES scans of the formation of ZnO in
aqueous solution. We have a series of scans from this experiment and I
have done a PCA on them using SIXPack. After doing the PCA I unchecked
the components until I could no longer visually reconstruct the series
of scans accurately (by visual determination). Using this visual
method I only need 2 components. But if I go by the minimum of the IND
function (what the SIXPack user guide recommends) I should use three

I have posted the sample/reconstruction plots for 2 and 3 component
reconstructions here (the scan I chose to reconstruct is
representative of the data series):


The main difference between the two plots is that the 3 component
reconstruction fits the edge region better. Zoom in (hold down the
right mouse button) and you'll see what I'm talking about. That said I
really have my doubts about 3 components being necessary, the visual
differences are so slight that I can't help but think that these
differences are just part of the noise. As for 2 or 3 components being
physically possible, both are feasible give the chemistry involved.

SIXPack does not provide IE or F test, so I plotted the IND results
vs. number of components for all the reactions. Except for the lowest
concentration the IND value reached a minimum at 3 components for all
the reactions. You can see the plot of IND value vs. number of
components here:


The IND minimum is rather broad. Are there other techniques that I
should be using to determine the number of components from the PCA? I
look forward to your feedback.

Kevin McPeak
kmm333 at drexel.edu
PhD Candidate
Chemical Engineering
Drexel University

P.S If you use Firefox or Safari you can zoom in on these plots by
holding down the right mouse button and making a box. Release the
right mouse button to zoom in on that box. Press the left arrow button
to the left of the plot to un-zoom.
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