Anurag, I assume you are doing one GPA for the combined data and not combining the data after GPA has been performed separately on both subsets. The latter surely could lead to the problem you describe.
I recommend, if you have not done so already, using the plotOutliers function. It will provide specimen numbers for outliers. Then you can use plotRefToTarget, following the examples in the help file but with your data and the specific specimen numbers that concern you, so that you can get a visual idea of why these specimens are divergent in shape from the others. You should be able to ascertain whether there was a procedural error (like flipping the order of two landmarks), digitizing bias (like one person tends to put landmarks more to the left, and another more to the right for vague anatomical points), or natural variation (maybe the specimens are just different). There is nothing in the gpagen function - or Generalize Procrustes analysis, in general - that would inherently introduce a bias to only certain configurations. Good luck solving this! Michael Collyer Associate Professor Biostatistics Department of Biology Western Kentucky University 1906 College Heights Blvd. #11080 Bowling Green, KY 42101-1080 Phone: 270-745-8765; Fax: 270-745-6856 Email: michael.coll...@wku.edu<mailto:michael.coll...@wku.edu> On Jun 27, 2016, at 1:45 PM, Anurag Mishra <anuragmishra1...@gmail.com<mailto:anuragmishra1...@gmail.com>> wrote: I had assigned landmarks to a group of specimen images (lizard heads) in tpsDIG and stored them as a .TPS file. I later wished to add a few more samples (of specimens from other locations, images photographed by others that were sent to me via mail) so I added the same landmarks in the same order and appended the new specimens to my existing .tps file. However, after applying a Generalized Procrustes Analysis (gpagen function in Geomorph package), when I generate a PCA plot, I get the new samples as outliers. I am quite positive that the newly acquired specimens should not be so different from the data I already had. Is there anything I am doing wrong? To my understanding, the images being taken by different sources should not matter because gpagen function transforms all the landmarks orientations to represent only shape data. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org<http://www.morphometrics.org/> --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org<mailto:morphmet+unsubscr...@morphometrics.org>. -- MORPHMET may be accessed via its webpage at http://www.morphometrics.org --- You received this message because you are subscribed to the Google Groups "MORPHMET" group. To unsubscribe from this group and stop receiving emails from it, send an email to morphmet+unsubscr...@morphometrics.org.
