If the artifact of preservation is a simple bending of the entire shape then you may wish to consider the unbending option in tpsUtil. It was developed for some fossil fish data where several points were recorded along the backbone to detect cases in which the specimens were distorted - having a backbone that was not more or less straight. The tpsUtil program fits a quadratic to these points and then smoothly unbends the entire shape so as to straighten the backbone.
I think this is a much safer strategy than hoping that the first PC measures only distortion (just as the first PC is not always a very safe measure of general size). F. James Rohlf [EMAIL PROTECTED] 03/17/2003 > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] Behalf Of > [EMAIL PROTECTED] > Sent: Monday, March 17, 2003 11:59 AM > To: [EMAIL PROTECTED] > Subject: Re: question on the use of relative warp scores for statistical > > > Kristel, > We have found precisely the same thing. RW1 often is obviously a > fixaton effect. We informally refer to this shape axis as "bendiness" > and I'm sure I know precisely what it looks like even in your fish, as > we have seen it in so many species in my lab. > > Your suggested use of RW1 as a covariate seems perfectly acceptable to > me. The only problem is justifying that RW1 really is a fixation > effect. I agree that enough experience seeing it makes it very obvious > that is what is going on, but there is no way I can think to rigorously > document this within the context of a given sample. (And sometimes RW1 > may also contain allometry and some other things mixed in with the > fixation effect). > > It may be possible to justify externally that the RW1 axis is a fixation > effect. Once could do this experimentally, by derriving an axis > separating two sets of images where one set is from live fish and the > second set is from those same fish after formalin fixation. If that > canonical (MANCOVA) axis looks very much like your RW1, then you have a > nice external justification. > > I don't think there is a statistical problem with using RW1 as a > covariate in MANCOVA. Although RW1 is generated in the framework of > PCA, the significance test is really not of interest. The PCA in this > case is just a tool to make a measurement. > > Please share the responses you get from your query, as this is an > interesting problem of fairly general concern. > > Thom DeWitt > > _______________________________ > > Dr. Thomas J. DeWitt, Assistant Professor > Department of Wildlife & Fisheries Sciences > & Program in Bioenvironmental Sciences > Texas A&M University > 2258 TAMU > College Station, TX 77843-2258 > > Tel. (979) 458-1684 (office) > Tel. (979) 845-7522 (lab) > Fax (979) 845-4096 > E-mail [EMAIL PROTECTED] > Web http://wfscnet.tamu.edu/wfscnet/facstaff/tdewitt/webpage.htm > TAMU Map to DeWitt lab & office: > http://www.tamu.edu/map/gifs/detail/FGHB.gif > > >>> <[EMAIL PROTECTED]> 03/11/03 03:24PM >>> > analysis > Sender: [EMAIL PROTECTED] > Precedence: bulk > > Hi everybody > > > > I was wondering if anybody had some comments on the following dilemma. > We are currently performing a tps analysis of body shape and possible > left-right differences in a cichlid fish, and we have come across the > following situation. It appears that relative warp 1 depicts a possible > = > artefact due to formalin fixation, which of course we would like to > filter out. > > 1. We would like to know whether we can treat RW1 as you would treat > PC1, depicting size, in a PCA, and thus immediately focus on RW2 plotted > against RW3. > > 2. Could we consider RW1 as an independent variable in a statistical > analysis, such as a MANCOVA, in which we would treat RW1 as a covariable > and partial warps as variables? Would it be correct to perform this kind > of analysis on the relative warp scores, taking into account that these > scores are already the result of a statistic analysis, based on these > partial warp scores? Can we somehow tease out the "effect" of RW1? > > > Thanks in advance, > > > > Kristel Wautier > Ghent University > Department of Biology > K.-L. Ledeganckstraat 35 > 9000 Ghent > Belgium > > Tel.: +32 9 264 52 31 > Fax: +32 9 264 53 44 > > [EMAIL PROTECTED] > http://allserv.rug.ac.be/~kwautier/VMDB/homepage.html > == > Replies will be sent to list. > For more information see http://life.bio.sunysb.edu/morph/morphmet.html. > == > Replies will be sent to list. > For more information see http://life.bio.sunysb.edu/morph/morphmet.html. == Replies will be sent to list. For more information see http://life.bio.sunysb.edu/morph/morphmet.html.
