Dear Rooney, I read your email very quickly. However, if you want to test and visualize differences between two groups, I guess you can use a discriminant analysis with all your shape variables and then regress your aligned (and projected in the tg space) coordinates onto the discriminant scores. The DA and multivariate regression can be done with most standard statistical software. Then, you can import predictions of the regression in Morphologika and you will be able to visualize the variation according to the axis that maximizes group differences. There are several other methods to test group differences (for instance with resampling statistics), and some issues on DA and related techniques when applied to shape variables. Give a look at Klingengerg & Monteiro, 2005, Syst. Biology. Good luck
Andrea >Hello all, > >I was hoping someone could give me guidance as to the correct course of >action, >when using GPA followed by PCA to describe difference in form >between 2 subgroups. Any assistance would be greatly appreciated! > >I have a dataset of 200 surface 3-D bone models, from which I have taken >seventeen representative 3-D landmarks. The dataset contains Asian/ >Caucasian, Female/ Male, and healthy/ osteo-arthritic specimens. I wish to >describe the differences in form caused by these factors. > >I have decided to analyse them in the following way. I have registered all 200 >specimens simultaneously, using GPA. I have outputted the corresponding PC >scores for PC1-PC6 (90% of variance) for each specimen. I have calculated the >average PC scores for each subgroup described above, for PC1-PC6. I have used >ANOVA on the PC-scores to identify which PCs (if any) distinguish >significantly between subgroups. >Alternatively, I could register all (say) Caucasians with one GPA, then >register all Asians with a separate GPA, arriving at the mean configuration >for >each group. Procrustes Analysis, followed by PCA could then be applied >to these 2 mean forms, in order to describe the modes of variation between >them. ANOVA obviously could not be carried out on the output in this >instance, given PC scores for just 2 specimens. Any difference described by >PCs >could not be verified statistically, using this method, I dont think? >Which of these 2 approaches would you recommend for describing form >difference, in terms of its PCs? > >Additionally, in an effort to generate a surface 3-D model representing each >subgroup for further analysis (eg. average Asian and average Caucasian), the >surface model of the most normal bone was identified (ie. the specimen whose >configuration is closest to the GPA mean configuration/ specimen whose PC >scores are closest to zero), then this model was warped to the average >PC1-PC6 scores for each subgroup. I am able to write out these average >surface models for each subgroup, along with their corresponding mean >landmark configuration. For this analysis, I have decided that, for >instance, the Asian and Caucasian average models should be generated by >using the same base model (be it Asian or Caucasian) and warping it to the >respective PC means of each ethnic subgroup. The alternative option is to >model the average Asian using a close-to-normal Asian base model and to >model the average Caucasian using a close-to-normal Caucasian base model. >Although each mean model thus generated would be true to its origins as it >were, I fear that to do it this way would be to introduce the difference >between the 2 base models, additional to the essential difference in ethnic >subgroups, as described by the difference in PC-score averages. Which of >these 2 approaches would you recommend? > >Many many thanks! > >Niall Rooney > >-- Replies will be sent to the list. >For more information visit http://www.morphometrics.org > > > Dr. Andrea Cardini Hull York Medical School The University of York, Heslington, York YO10 5DD, UK & The University of Hull,Cottingham Road, Hull HU6 7RX, UK tel. 01904 321752 fax 01904 321696 E-mail: [EMAIL PROTECTED] http://www.york.ac.uk/res/fme/people/andrea.htm ------------------------------------------------------------------------- Visita http://domini.interfree.it, il sito di Interfree dove trovare soluzioni semplici e complete che soddisfano le tue esigenze in Internet, ecco due esempi di offerte: - Registrazione Dominio: un dominio con 1 MB di spazio disco + 2 caselle email a soli 18,59 euro - MioDominio: un dominio con 20 MB di spazio disco + 5 caselle email a soli 51,13 euro Vieni a trovarci! Lo Staff di Interfree ------------------------------------------------------------------------- -- Replies will be sent to the list. For more information visit http://www.morphometrics.org
