Hi,

I want to follow up on this. We want to use the PC scores from the shapeworks analysis as input for our quantitative trait mapping to find genomic intervals associated with molar morphology and size. We successfully used this approach using traditional landmarks, but I definitely see value using SW. However, there are couple concerns:

1.      We are not getting repeatable results (as Ryan described below) with identical datasets and parameter xmls. Parameter space is too big to randomly experiment on our own. We can use suggestions on what to focus and what might be driving this randomness.

2.      Although I can visualize the modes of variation using SW Studio, I can’t get to the individual eigenvectors or the PC scores. To overcome this, I am feeding the wpts files into a Procrustes analysis and doing alignment and PCA, which is kind of silly, since SW does it already. It would be good to expose the PC scores an eigenvectors.

Best wishes,

Murat

A. Murat Maga, PhD

Assistant Professor

UW Dept. of Pediatrics

Division of Craniofacial Medicine

&

Member

Seattle Children’s Research Institute

Center for Developmental Biology and Regenerative Medicine

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