Re: [MORPHMET] Does a research sample need to be normally distributed (male/female ratio) for PCA?
Thank you for the explanation James. So that is why the ellipse is migrating towards the species 3 even though it does not have male species. Regards, Helmi On Sunday, May 28, 2017 at 11:01:30 AM UTC+8, K. James Soda wrote: > > Dear Dr. Hadi, > > I would just like to add one additional comment to your question about the > need for normal distributions in PCA. Dr. Mitteroecker is (of course) > correct that PCA does not make any distributional assumptions, but you > mentioned in passing that confidence ellipses are being placed around the > points. Confidence ellipses usually do assume that the data is > multivariate normal. There are distribution-free methods for placing > confidence intervals, but my suspicion is that these intervals would not > usually have an elliptical appearance unless the data was in fact normally > distributed. > > So to reiterate: PCA, no distributional assumptions. Confidence > ellipses, usually assume multivariate normal data. > > Hope that comment is useful, > > James > > On Thu, May 25, 2017 at 4:58 AM, Helmi Hadi > wrote: > >> Dear morphometricians, >> >> Does a sample need to be normally distributed when conducting PCA in >> geometric morphometrics? Sometimes due to research constraints there are no >> samples of the opposite sex. Someone was asking me this question, and I do >> not have the answer. When I look at the data distribution, there is quite >> an imbalance male/female population. However, the classifiers male/female >> and species are there and you can sort of tell which group belongs to >> where. My only fear is that the confidence ellipse for the males are being >> "gravitated" towards the females for one species as that species does not >> have any male specimens. Attached are the file which I have recreated the >> dataset based on memory. >> >> Is this kind of data acceptable or publishable? >> >> My own personal question is based on the GMM results given in MorphoJ. >> The PC1/PC2 axes does not intersect at the middle (which I have personally >> drawn the dotted line there). I don't mind this output, but does it matter >> to have the axes cut at the 0 value? The data data distribution does not >> change with the change of axes lines. I noticed some GMM papers have the >> axes at 0. >> >> Thanks all for the help, >> >> Helmi Hadi, >> School of Health Scienes, >> Universiti Sains Malaysia >> >> -- >> 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+u...@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.
Re: [MORPHMET] Does a research sample need to be normally distributed (male/female ratio) for PCA?
Dear Dr. Hadi, I would just like to add one additional comment to your question about the need for normal distributions in PCA. Dr. Mitteroecker is (of course) correct that PCA does not make any distributional assumptions, but you mentioned in passing that confidence ellipses are being placed around the points. Confidence ellipses usually do assume that the data is multivariate normal. There are distribution-free methods for placing confidence intervals, but my suspicion is that these intervals would not usually have an elliptical appearance unless the data was in fact normally distributed. So to reiterate: PCA, no distributional assumptions. Confidence ellipses, usually assume multivariate normal data. Hope that comment is useful, James On Thu, May 25, 2017 at 4:58 AM, Helmi Hadi wrote: > Dear morphometricians, > > Does a sample need to be normally distributed when conducting PCA in > geometric morphometrics? Sometimes due to research constraints there are no > samples of the opposite sex. Someone was asking me this question, and I do > not have the answer. When I look at the data distribution, there is quite > an imbalance male/female population. However, the classifiers male/female > and species are there and you can sort of tell which group belongs to > where. My only fear is that the confidence ellipse for the males are being > "gravitated" towards the females for one species as that species does not > have any male specimens. Attached are the file which I have recreated the > dataset based on memory. > > Is this kind of data acceptable or publishable? > > My own personal question is based on the GMM results given in MorphoJ. The > PC1/PC2 axes does not intersect at the middle (which I have personally > drawn the dotted line there). I don't mind this output, but does it matter > to have the axes cut at the 0 value? The data data distribution does not > change with the change of axes lines. I noticed some GMM papers have the > axes at 0. > > Thanks all for the help, > > Helmi Hadi, > School of Health Scienes, > Universiti Sains Malaysia > > -- > 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. > -- 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.
[MORPHMET] Does a research sample need to be normally distributed (male/female ratio) for PCA?
Dear morphometricians, Does a sample need to be normally distributed when conducting PCA in geometric morphometrics? Sometimes due to research constraints there are no samples of the opposite sex. Someone was asking me this question, and I do not have the answer. When I look at the data distribution, there is quite an imbalance male/female population. However, the classifiers male/female and species are there and you can sort of tell which group belongs to where. My only fear is that the confidence ellipse for the males are being "gravitated" towards the females for one species as that species does not have any male specimens. Attached are the file which I have recreated the dataset based on memory. Is this kind of data acceptable or publishable? My own personal question is based on the GMM results given in MorphoJ. The PC1/PC2 axes does not intersect at the middle (which I have personally drawn the dotted line there). I don't mind this output, but does it matter to have the axes cut at the 0 value? The data data distribution does not change with the change of axes lines. I noticed some GMM papers have the axes at 0. Thanks all for the help, Helmi Hadi, School of Health Scienes, Universiti Sains Malaysia -- 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.
