-----Original Message-----
From: morphmet [mailto:[email protected]]
Sent: Thursday, March 31, 2011 11:23 AM
To: morphmet
Subject: Re: [Fwd: Re: Morphometrics of small, variable specimens--
embryos]
-------- Original Message --------
Subject: Re: [Fwd: Re: Morphometrics of small, variable specimens--
embryos]
Date: Wed, 30 Mar 2011 18:09:30 -0400
From: [email protected]
To: [email protected]
Andrea,
Thanks for this.
Regarding my second post, I can restate the issue more succinctly.
I correct the data by regressing the Procrustes coordinates on centroid size. I
further correct the data for developmental stage by regressing the centroid
size residuals on somite number.
This should remove variation correlated with size and with developmental
stage, at least to the degree a linear model will allow.
The PC1 scatter of the data are such that early and late stage embryos cluster
together toward one end and intermediately staged embryos are scattered
toward the other.
How interpretable is the wireframe deformation in a case like this, where at
one extreme of the major linear trend both early and late staged embryos
are found together. The shape change along PC1 relates to ontogeny, but
not in a simple straight forward way. The earlier and late staged embryos are
very different from on another, and this can be seen just by eye, yet they
occupy the same region of PC1. PC2 is similar in this pattern but not as
severe.
Do these observations say that there is still a strong non-linear component of
variation in my data that the above corrections leave behind?
Is it correct to interpret a wireframe scaled to the area occupied by both
developmentally old and young embryos as a composite of features typical
of each stage?
Eric
>
>
> -------- Original Message --------
> Subject: Re: [Fwd: Re: Morphometrics of small, variable
> specimens--embryos]
> Date: Wed, 30 Mar 2011 03:52:13 -0400
> From: andrea cardini <[email protected]>
> To: [email protected]
>
> A quick comment on errors, Eric, besides what David told you.
> By repositioning the specimen you will be able to get also that source
> of error in the model. Then, you can test the total error or do the
> test after partitioning it between positioning and digitizing error,
> as Daid suggested and can be easily done in MorphoJ. However, this
> won't do much to tell you how good the 2D approximation of your 3D
> structures is. To add that you would need 3D measurements (at least on
> a subsample of specimens). You can possibly try to minimize this error
> by choosing almost coplanar landmarks.
>
> About your second question, I read the message quickly and I am not
> sure about what exactely you're doing. Generally, if your aim is to
> compare groups by holding the effect of a covariate constant, a fairly
> traditional approach would be a MANCOVA (or its version using
> resampling stats).
> There's an example about this in the context of allometry in the help
> file of TPSRegr (test for common slope and homogeneity of intercept)
> and the method is related to MorphoJ's 'size-correction', I believe.
>
> Good luck.
> Cheers
>
> Andrea
>
>
>
> At 12:13 29/03/2011 -0400, you wrote:
>>
>>
>>-------- Original Message --------
>>Subject: [Fwd: Re: Morphometrics of small, variable
>>specimens--embryos]
>>Date: Tue, 29 Mar 2011 12:06:03 -0400
>>From: [email protected]
>>To: [email protected]
>>
>>---------------------------- Original Message
>> ----------------------------
>>Subject: Re: Morphometrics of small, variable specimens--embryos
>>From: "P. David Polly" <[email protected]>
>>Date: Tue, March 29, 2011 10:02 am
>>To: [email protected]
>>----------------------------------------------------------------------
>>----
>>
>>You might get part of the error by removing one of the PCs, but that
>>approach is less precise than partitioning it out. The PC axes are
>>simply axes of greatest variation so they are not directly associated
>>with any causal process (including mounting error). Error due to
>>mounting may be concentrated on one PC axis, but it may be spread
>>across more than one, plus non-error may also contribute to the same
>>PC axis (e.g., true bilatral asymmetry might logically contribute to
>>shape variation in exactly the same way as error in the saggital
>>section).
>>
>>The ANOVA approach is equivalent to regressing out the error (ANOVA
>>and regression are in some senses the same thing, one for factor
>>variables and the other for continuous variables). With the ANOVA
>>you know you are removing only variation due to the mounting, and you
>>also know you are removing most of it (to the extent that two
>>mountings per specimen are representative of the amount of the total
>>amount of error).
>>
>>
>>
>>----- Original Message -----
>>From: <[email protected]>
>>To: "P. David Polly" <[email protected]>
>>Sent: Tuesday, March 29, 2011 11:55 AM
>>Subject: Re: Morphometrics of small, variable specimens--embryos
>>
>>
>>> Thanks! What about regressing the data on a PC that appears to
>>> explain mounting errors?
>>>
>>> Eric
>>>
>>>> Hi Eric,
>>>>
>>>> I think you're on the right track with mounting the same specimen
>>>> more than once. If you do every specimen two or three times you
>>>> can partition out the shape variation due to mis-alignment of the
>>>> plane. To do this you add an additional level to your ANOVA so
>>>> that it has factors for between group, between individual, and
>>>> between mount variation. There are several papers you can cite for
>>>> this method, but my favourite is Baily and Byrnes, 1990.
>>>> A
>>>> new, old method for assessing measurement error in both univariate
>>>> and multivariate morphometric studies. Syst. Zool. 39: 124-130.
>>>>
>>>> Best wishes,
>>>> David
>>>>
>>>> -----------------------
>>>> Dr. P. David Polly
>>>> Department of Geological Sciences
>>>> Indiana University
>>>> 1001 E. 10th Street
>>>> Bloomington, IN 47405 USA
>>>> [email protected]
>>>> +1 812 855 7994
>>>> http://mypage.iu.edu/~pdpolly/
>>>>
>>>> (Adjunct in Biology and Anthropology)
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: "morphmet" <[email protected]>
>>>> To: "morphmet" <[email protected]>
>>>> Sent: Tuesday, March 29, 2011 11:36 AM
>>>> Subject: Morphometrics of small, variable specimens--embryos
>>>>
>>>>
>>>>>
>>>>>
>>>>> -------- Original Message --------
>>>>> Subject: Morphometrics of small, variable specimens--embryos
>>>>> Date: Tue, 29 Mar 2011 10:28:14 -0400
>>>>> From: [email protected]
>>>>> To: [email protected]
>>>>>
>>>>> Hello all,
>>>>>
>>>>> I am currently doing 2D and 3D analyses of midgestational mouse
>>>>> embryos.
>>>>> My sample is variable owing to ontogenetic variation. Genetic
>>>>> variation is very minimal, as my strains are mostly congenics,
>>>>> having practically identical genetic backgrounds but differing
>>>>> only at one or two loci.
>>>>> The
>>>>> specimens are also very small.
>>>>>
>>>>> First, for the 2D analysis, I am photographing freshly harvested
>>>>> and unfixed embryos in three different orientations (top, lateral,
>>>>> and "frontal" = palatal view), mounting in a petri dish of cold
>>>>> saline and photo'ing two separate times per view. Each set of
>>>>> images per specimen is landmarked twice, and all the data will be
>>>>> subject to an initial procrustes ANOVA to assess the relative
>>>>> strengths of the different effects of mounting, landmarking,
>>>>> genotype, and specimen. However, I expect, and experience shows,
>>>>> that a significant portion of the variance in the data will be due
>>>>> to mounting errors. The embryos are small and difficult to
>>>>> position. GPA will take care of rotational errors. But slight
>>>>> rotations out of the plane (pitch and yaw) will produce variation
>>>>> in the data that will look like shape variation. My hope is that
>>>>> by mounting and photo'ing twice, I will reduce pitch/yaw errors.
>>>>>
>>>>> Will the mean square of the mounting effect reflect the amount of
>>>>> those types of errors?
>>>>>
>>>>> If I can identify a PC that appears to capture pitch or yaw, can I
>>>>> regress the procrustes coordinates on that PC in order to remove
>>>>> those errors from the data?
>>>>>
>>>>> Thanks.
>>>>>
>>>>> Eric
>>>>>
>>>>> [email protected]
>>>>> University of Calgary
>>>>> Faculty of Medicine
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>>
>>
>>
>>
>>
>
> Dr. Andrea Cardini
> Researcher in Animal Biology
> Dipartimento di Biologia, Universitá di Modena e Reggio Emilia, via
> Campi 213, 41100, Modena, Italy
> tel: 0039 059 2055017 ; fax: 0039 059 2055548
>
> Honorary Fellow
> Functional Morphology and Evolution Unit, Hull York Medical School
> University of Hull, Cottingham Road, Hull, HU6 7RX, UK University of
> York, Heslington, York YO10 5DD, UK
>
> Adjunct Associate Professor
> Centre for Forensic Science , The University of Western Australia
> 35 Stirling Highway, Crawley WA 6009, Australia
>
> E-mail address: [email protected], [email protected],
> [email protected]
>
> Webpage: http://sites.google.com/site/hymsfme/drandreacardini
> Datasets:
>
http://ads.ahds.ac.uk/catalogue/archive/cerco_lt_2007/overview.cfm#met
> adata
>
>
>
>
>
