Hi Anderson,
I concur with Murat about the usefulness of having actually multiple
specimens. Analyses on a single specimen, although in principle
attractive (as one "isolates" error from biological variation), are not
necessarily informative on a practical level. Also there are two
problems, one of magnitude (e.g., how large is variation due to
distance/presentation relative to biological variation), one of
direction (e.g., if one distance/presentation gets consistently
digitised differently from the other, that is, you have non-random
error/bias). You can find discussions of these in my recent review which
Murat very kindly suggested.
I would add that, in addition to the digitization process, differences
might have been caused by factors. However, another thing that I noticed
in your TPS file is that you have first all the repetitions at one
distance, then all the others. So I assume you digitized them in that
order. This suggests that, as already pointed out by Murat, the
differences might be due to "learning" or changes over time in the way
you digitize.
Most likely, the final error will come from a combination of various
sources, as it's generally the case.
In general, I would suggest you to run a larger preliminary analysis with:
- multiple biological specimens
- multiple distances
- multiple digitizations
- digitizing in random order across repetitions (there is a very useful
function for this in tpsUtil by F.J. Rohlf)
- using multiple statistical tools to gauge how large is the error
relative to biological variation and if there are non-random patterns
I hope this helps,
Carmelo
Il 2/01/2018 7:28 PM, Murat Maga ha scritto:
Hi Anderson,
I don’t think PCA is the tool you want to use in this context.
Procrustes anova already tells you that your two magnification levels
are done differently. Since your question is ‘can I combine data from
different magnification level in the same analysis?’, the answer to
that in your current study design (single sample measured five times
at two different scales) is a very qualified no.
But, what is more relevant, (or what I would have liked to know) the
magnitude of this error in context of actual biological variation.
For that, you have to have a study design where you have a few samples
of different sizes measured at different magnification scales a couple
times (not just measuring the same object repeatedly in different
magnifications), or something along those lines.
There is a really a lot of literature on this. But you need to use a
statistics based framework, not EDA tools like PCA to answer this.
M
*From:* Anderson Feijo [mailto:andefe...@gmail.com]
*Sent:* Monday, January 1, 2018 11:02 PM
*To:* Murat Maga <m...@uw.edu>
*Cc:* MORPHMET <morphmet@morphometrics.org>
*Subject:* Re: [MORPHMET] Doubt Scaling photos
Dear Murat,
Thank you very much for your email and time for explore my dataset. To
perform this simple experiment, given the aim was to explore the
magnification issue, I chose only three landmarks (as you could see in
the tps file) easily to replicate. The reason I am trying to combine
two magnification is that I will work with groups with different
sizes; for example, species with 10 cm and others with 3 cm of total
length of skull. Place the camera at a good distance to avoid parallax
for the large group will lead a low resolution images of the small
groups. Thus, my initial idea was to have two standardized distances
and combine later after accounting the scale effects.
In my short experiment, what intrigues me is the clear groups in PCA
(and other exploratory analyses) based on the two magnifications (see
below). At the beginning, I was expecting a great overlap between the
two distances and minimum differences due to landmarks-placement error
as seen within each of the group.
Best,
Anderson
Inline image 1
On Sat, Dec 30, 2017 at 3:57 PM, Murat Maga <m...@uw.edu
<mailto:m...@uw.edu>> wrote:
Dear Anderson,
It has nothing to do with the scale of your data (or least not
directly).
As you can see, you actually performed those two digitization
attempts differently. It is maybe 1-2 pixels off, but in a very
consistent way (greens are from one scale, red is the other scale,
and cross is the consensus shape). This type of systematic error
commonly occur in digitization process, as one learns better or
alters the way landmarks are digitized/defined along the process.
In your case, perhaps higher resolution image gave a better
definition (imaging sense) of landmarks, so you captured them very
slightly differently than low-res image (but in a very consistent
way).
If you are concerned, the first step perhaps is to do the same
thing (i.e. digitization of same sample with different
magnifications several times) with several real specimens and get
a sense of the magnitude of this error in context of the
biological variation. Then perhaps you can decide, whether you can
actually combine digitization’s from different magnification
levels. There is quite a bit of literature on this, you can start
with a recent review.
https://www.ncbi.nlm.nih.gov/pubmed/27038025
Is there a reason you are not using a single magnification level
for all your samples?
M
*From:* Anderson Feijo [mailto:andefe...@gmail.com
<mailto:andefe...@gmail.com>]
*Sent:* Friday, December 29, 2017 1:35 AM
*To:* MORPHMET <morphmet@morphometrics.org
<mailto:morphmet@morphometrics.org>>
*Subject:* [MORPHMET] Doubt Scaling photos
Hi everyone,
I am starting a new project using GM working with groups with
different sizes (eg. rodents and small carnivores). I would like
to use the whole dataset combined in the analyses, instead of
perform set of analyses for each sized group. So, I did a test
using the same skull and place the camera in two distance to the
object (~15 cm and ~30 cm). My expectation was after scaling
(using tpsDig) I wouldn´t detect any meaningful difference in the
dataset. However, I got two clear groups that were even
statistically different. I have attached here the tps file that I
used (10 copies of the same skull, 5 at ~15 cm and 5 at ~30cm). My
question is how can I combine two set of 2d landmarks based on
photos taken from different distance to the object. I would
greatly appreciate any suggestion.
All the Best and Happy 2018!
Anderson
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Dr. Anderson Feijó
Key Laboratory of Zoological Systematics and Evolution
Institute of Zoology, Chinese Academy of Science
Beichen West Road, Chaoyang District, 100101
Beijing, China
Curriculum: /Lattes <http://lattes.cnpq.br/9406413385468571>;
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