how to make a PCA?

[Jana]

Could somebody recommend simple software or online app to make it?
Tried downloading few pro apps, but they are too complicated to use for me.

Thanks.

[Karol Klačansky]

I use R. I can send you my code for the R program for my Eurogenes EU pca plot if you want.

its not that difficult but there are probably simpler pca creating tools online.

[JamesBond007]

Could somebody recommend simple software or online app to make it?
Tried downloading few pro apps, but they are too complicated to use for me.

Thanks.

PAST is easier than R. Open datasheet with PAST and choose Multivariate > Ordination > Principal Components Analysis. You might or might not have to select all the data cells first after opening it I can't remember.

https://folk.uio.no/ohammer/past/

Caveat : only works on windows and mac not on Linux etc..

[Jana]

PAST is easier than R. Open datasheet with PAST and choose Multivariate > Ordination > Principal Components Analysis. You might or might not have to select all the data cells first after opening it I can't remember.

https://folk.uio.no/ohammer/past/

Caveat : only works on windows and mac not on Linux etc..

I try to use exactly that one, but still no clue.

[Peterski]

Now there is already PAST4 - https://folk.uio.no/ohammer/past/

[Jana]

I need instrcutions, obviously.

[Peterski]

First prepare a datasheet in Excel, Libre Office Calc or Open Office Calc and then copy-paste it into PAST.

[pulstar]

I use Python's sklearn for that, but since you said you look for simple software I guess that's not an option :)

[Lucas]

Could somebody recommend simple software or online app to make it?
Tried downloading few pro apps, but they are too complicated to use for me.

Thanks.

in PAST

I write about Menu option in next steps:

1.
https://i.imgur.com/feeIYjr.jpg

2. Edit > Paste (here you paste data from excel sheet), click in first cell of column Name (which appears after doing above). I suppose you have your data in excel like that
https://i.imgur.com/BqZoyKk.png

3. After paste data, Edit>Select all

4. Multivariate > Ordination > PCA

https://i.imgur.com/WcQsJah.png

[Karol Klačansky]

here I sent these instructions to my father once on how to make a pca plot in PAST. I explained every step of it. Try it also with the data set that is provided by Davidski from the link and then follow the instructions.




http://eurogenes.blogspot.com/2018/05/global25-workshop-2-intra-european.html

1)first download Past software
2)download G25 datasheet with european population
3) open european datasheet in Past3 program and then click blank space above variable names, which highlights the entire data set
4) click on multivariate button on top of program, and then click ordination and then PCA
5) in new window click on scatter plot and then tick the empty boxes on right "Group labels" "Convex hulls" also go to Graphic settings and click filled regions.

[Peterski]

I sent my intstructions in PMs.


filled regions.

Yes this is also a useful option.
(forgot to mention in my PMs)

Also e.g. Grid can be added.