Celine, as Dr. Hammer has pointed out, check the starting position and rotation of your images in Past. I cannot exactly remember what was the origin of the problem in terms of data recording, but one of our students had a similar problem when using EFA (I think) and SHAPE. At least the symptoms were the same: a huge difference in the variance explained, which was higher in the EFA PC1. When we looked at the graphic representation of the first principal component from the EFA data, we realized that it was merely expressing the orientation of the structure (i.e. if it was "pointing to the left or to the right"). So orientation (determined by rotation and starting point) of course accounted for most of the variability (and the variance explained was much higher, because we had entered an artifact resulting in extra variance). When the origin and alignment were properly specified in SHAPE (i.e. all the images were "pointing in the same direction"), the variance explained was lower, but the principal components were expressing meaningful shape differences.
Hope this helps, Luis ________________________________ Luis Cabo Mercyhurst Archaeological Institute, Mercyhurst College, Erie, PA E-mail: [EMAIL PROTECTED] ----- Original Message ----- From: "morphmet" <[EMAIL PROTECTED]> To: "morphmet" <[email protected]> Sent: Thursday, June 07, 2007 11:11 AM Subject: Re: Fourier > Hi, I'm the author of PAST. The EFA algorithm in PAST > is the one described in this paper: > > Ferson, S.F., F.J. Rohlf & R.K. Koehn. 1985. > Measuring shape variation of two-dimensional outlines. > Systematic Zoology 34:59-68 > > I don't know Shape. However, one possible source for > the difference is the standardization procedure - > whether, and if so how, the program standardizes for > size, rotation and the starting position for digitization. > > Did you tick the "Invariant to rotation and starting > position" box in PAST? > > And as Dennis Slice said - check whether the PCA > standardizes for variance ("PCA on the correlation > matrix"). > > It would also be interesting if you could test > Rohlf's EFA program, which should give similar > results as PAST (?). > > > Regards, > > Oyvind Hammer > Natural History Museum > University of Oslo > > > On Thu, 7 Jun 2007, morphmet wrote: > >> Dear morphometricians, >> >> I'm doing some research on headshape dimorphism in European Eel using >> elliptic Fourier analysis. >> I've used the programs TPSUtil and TPSDig to get the coordinates of the >> contours of the heads and then used the program PAST to analyze these >> (with PCA). >> I've also used the program Shape on the same specimens, but the results >> were different. >> >> When I used Shape the first principal component explained about 48% of >> the variance, but when I used PAST the first PC explained 66% of the >> variance. >> >> Is there anyone who can explain this difference and maybe tell me which >> method is the best to do a Fourier-analysis? >> >> Thank you in advance >> Celine Ide >> >> >> Ghent University >> Evolutionary Morphology of Vertebrates >> KL Ledeganckstraat 35 >> B- 9000 Ghent >> Belgium >> +32 92645220 >> [EMAIL PROTECTED] >> >> >> >> -- >> Replies will be sent to the list. >> For more information visit http://www.morphometrics.org >> >> > > > > -- > Replies will be sent to the list. > For more information visit http://www.morphometrics.org -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
