[Ifeffit] Ifeffit Digest, Vol 78, Issue 27

[Kevin McPeak]

Andreas,

Thanks for your input. We did you use a Zn foil reference and I had
aligned the scans in Athena using the auto align feature (to the
smoothed derivative). But do to your and Carlo Segre's suggestions I
re-checked the alignment, this time zooming very closely. I noticed
that a few of the reference scans were +/-0.1 eV misaligned from the
reference standard. After the re-alignment the IND value now reaches a
minimum at 2 components. Thanks so much for the suggestion! You really
can't be too careful with the alignment.

Kevin

On Fri, Aug 28, 2009 at 1:00 PM,
<ifeffit-request at millenia.cars.aps.anl.gov> wrote:
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>   1. Re: Determining the correct number of components from PCA
>      (Voegelin, Andreas)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 27 Aug 2009 23:12:12 +0200
> From: "Voegelin, Andreas" <Andreas.Voegelin at eawag.ch>
> Subject: Re: [Ifeffit] Determining the correct number of components
>        from PCA
> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID:
>        <9B57B672CD2140498D728E4524354F4264D5BF at EA-MAIL.eawag.wroot.emp-eaw.ch>
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> Content-Type: text/plain;       charset="us-ascii"
>
> 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,
>
> Andreas
>
> -----Original Message-----
> From: ifeffit-bounces at millenia.cars.aps.anl.gov
> [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Kevin
> McPeak
> 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
> components.
>
> 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):
>
> http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_2comp.
> html
> http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_recon_12.5_90_scan10_3comp.
> html
>
> 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:
>
> http://dunx1.irt.drexel.edu/~kmm333/xafs/pca_ind_results.html
>
> 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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> End of Ifeffit Digest, Vol 78, Issue 27
> ***************************************
>