-------- Original Message --------
Subject: Re: PCA results interpretation
Date: Tue, 27 Jul 2010 11:53:02 -0400
From: Kim van der Linde <[email protected]>
To: [email protected]
CC: morphmet <[email protected]>
Well, PC1 is often related to allometric variation, and it is logical
that this one is ignored if that is indeed the case. So, using PC2 makes
sense to me. The use of PC15 is not that strange, what is required is to
show that the factor explains a significant amount of the variation. If
they did so, and it corresponds with the grouping, I do not see an issue
with that. I suspect that some of the variation in PC2 relates to
females as well, but is dominated by the males in the sample while some
of the residual variation in the females pops out as the 15th PC.
Kim
On 7/26/2010 12:52 PM, morphmet wrote:
-------- Original Message --------
Subject: PCA results interpretation
Date: Mon, 26 Jul 2010 08:49:01 -0700
From: Murat Maga <[email protected]>
To: morphmet <[email protected]>
Dear morphometricians,
I was reading a paper which compared mid-face shape in the unaffected
parents of cleft-lip kids versus the age matched controls. Results (and
their interpretation) made me think about how far PCA scores can be (or
should be) utilized. They ended up using PC2 and PC15 to define and
visualize the difference between groups. I wouldn't expect the variation
contributed by the first group to the total variation to be too much,
they are almost normal after all. But using PC15 to define these
characteristics, could this be a bit of stretch? They only reported the
total variation accounted by these two components (14.5%). They said
none of the other PC showed evidence of group discrimination. I expect
PC15 has a minuscule contribution to this sum. So the question I have,
is it fair game to fish for PCAs as long as they provide the
discrimination you are looking between your groups. Obviously, results
don't have to be statistically significant to be biologically relevant.
And it is obviously very important to be able to detect people that look
normal, but has higher risk of having kids with cleft.
But at what point one would say, "yes, PC15 seems to separate them, but
could this be an artifact of my samples, or some random noise"?
Another statement made by the authors:
"This finding [according to authors PC2 separates unaffected male
parents from controls and PC15 does the same for females] was confirmed
by results showing that mean PC scores on the second component differed
significantly between unaffected fathers and male controls (p=.001)".
They have a similar statement for PC15 as well. I haven't heard the term
"mean PC scores" before? Are they talking about running an anova on the
PCs, by using groups as factors?
Thanks,
M
--
http://www.kimvdlinde.com
