G25 European PCA for Apricity users

[J. Ketch]

Same as the other thread, give me your scaled coordinates and I'll put you in if you plot within the European variation.

https://i.postimg.cc/bwD1t1F4/NWEuro1.png
https://i.postimg.cc/YSBLLZFm/East-Euro1.png

[Ayetooey]

Zoran23_scaled,0.133173,0.132019,0.046386,0.034561 ,0.037238,0.017012,-0.0047,0.007154,0.0045,-0.003645,-0.004709,0.000599,0.000297,-0.004542,-0.000543,0.01432,0.017732,0.006841,0.004525,0.0028 76,-0.003993,-0.001731,0.006902,0.01205,-0.000239

[Coastal Elite]

DacoCeltic_scaled,0.133173,0.13405,0.043369,0.0226 1,0.028313,0.01004,0.00235,0.004384,0.002863,0.006 014,-0.00747,0.008243,-0.014123,-0.004542,0.004072,-0.000796,0.001043,-0.00076,0.006913,-0.002876,-0.001123,0.004699,0.005423,0.00976,-0.005628

[J. Ketch]

Zoran23_scaled,0.133173,0.132019,0.046386,0.034561 ,0.037238,0.017012,-0.0047,0.007154,0.0045,-0.003645,-0.004709,0.000599,0.000297,-0.004542,-0.000543,0.01432,0.017732,0.006841,0.004525,0.0028 76,-0.003993,-0.001731,0.006902,0.01205,-0.000239
https://i.postimg.cc/pX16vYFS/ayetooey.png

[J. Ketch]

DacoCeltic_scaled,0.133173,0.13405,0.043369,0.0226 1,0.028313,0.01004,0.00235,0.004384,0.002863,0.006 014,-0.00747,0.008243,-0.014123,-0.004542,0.004072,-0.000796,0.001043,-0.00076,0.006913,-0.002876,-0.001123,0.004699,0.005423,0.00976,-0.005628
https://i.postimg.cc/4xsbrY80/dacocelt.png

[Cumansky]

Same as the other thread, give me your scaled coordinates and I'll put you in if you plot within the European variation.

https://i.postimg.cc/YSBLLZFm/East-Euro1.png

Intermediate of Estonian and Serbian I am located, see my GEDmatch, good work.

Using 2 populations approximation:
1 50% Estonian_+ 50% Serb_Serbia_ @ 2.313958

[Coastal Elite]

https://i.postimg.cc/4xsbrY80/dacocelt.png

Thanks!

[Bunalim]

Me

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
NW_scaled,0.113823,0.144205,0.006788,-0.014212,0.003693,0.009761,0.008695,-0.003,-0.02168,-0.006014,0.000325,0.008542,-0.020069,-0.000413,0.007465,-0.003845,-0.010561,0.007221,-0.000503,0.000125,0.001872,-0.001607,0.001725,0.008796,0.002754


My dad

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Dad_scaled,0.108132,0.14319,-0.04978,-0.062016,-0.031083,-0.013387,0.00893,-0.010153,-0.046427,-0.007472,0.008769,0.006444,-0.018137,0.004954,-0.0095,-0.005834,0.012647,-0.001647,-0.005908,0.002376,0.000749,0.005812,0.002342,-0.004579,-0.00455

My dad probably wont plot on the chart lol

[J. Ketch]

Me

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
NW_scaled,0.113823,0.144205,0.006788,-0.014212,0.003693,0.009761,0.008695,-0.003,-0.02168,-0.006014,0.000325,0.008542,-0.020069,-0.000413,0.007465,-0.003845,-0.010561,0.007221,-0.000503,0.000125,0.001872,-0.001607,0.001725,0.008796,0.002754


My dad

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Dad_scaled,0.108132,0.14319,-0.04978,-0.062016,-0.031083,-0.013387,0.00893,-0.010153,-0.046427,-0.007472,0.008769,0.006444,-0.018137,0.004954,-0.0095,-0.005834,0.012647,-0.001647,-0.005908,0.002376,0.000749,0.005812,0.002342,-0.004579,-0.00455

My dad probably wont plot on the chart lol
Correct, he's in the abyss.

https://i.postimg.cc/J45D9PHN/bunalim.png
https://i.postimg.cc/MpscGHDX/bunalim2.png

[J. Ketch]

PCA is now colourised like the Northern Euro version.

[Freeroostah]

VangosH_scaled,0.114961,0.148267,0.01697,-0.022287,0.020311,-0.00502,0.00329,0.005307,0.001227,0.007289,0.00568 4,0.000899,0.000297,0.01156,-0.010858,-0.012994,-0.004955,0.000253,0.008925,-0.01113,-0.005989,-0.003462,0.009244,-0.003374,-0.000479

Much appreciate it!

[Kaspias]

Thank you.

Kaspias_scaled,0.103579,0.08632,0.013199,-0.010982,-0.002462,-0.009761,0.00094,0.005077,-0.006136,0.000911,0.000162,-0.000749,0.002379,-0.005505,-0.012486,0.013524,0.015255,0.00152,0.007668,0.0043 77,-0.004866,-0.000247,0,0.010001,-0.002155

[J. Ketch]

VangosH_scaled,0.114961,0.148267,0.01697,-0.022287,0.020311,-0.00502,0.00329,0.005307,0.001227,0.007289,0.00568 4,0.000899,0.000297,0.01156,-0.010858,-0.012994,-0.004955,0.000253,0.008925,-0.01113,-0.005989,-0.003462,0.009244,-0.003374,-0.000479

Much appreciate it!


Thank you.

Kaspias_scaled,0.103579,0.08632,0.013199,-0.010982,-0.002462,-0.009761,0.00094,0.005077,-0.006136,0.000911,0.000162,-0.000749,0.002379,-0.005505,-0.012486,0.013524,0.015255,0.00152,0.007668,0.0043 77,-0.004866,-0.000247,0,0.010001,-0.002155

https://i.postimg.cc/GhyNSXxb/SEEuro1.png

[Kaspias]

I'm at the same line with Bulgarians, accurately. But my East Eurasian pulled me to downwards. Good work, thank you!

[Lemgrant]

I already know where I'm on this PCA. How about doing some clustering in PAST3 program? This is something that Davidski hasn't done for me.
https://i.imgur.com/BSChu8g.png

http://eurogenes.blogspot.com/2018/05/global25-past-compatible-datasheets.html

[Lemgrant]

Zoran23_scaled,0.133173,0.132019,0.046386,0.034561 ,0.037238,0.017012,-0.0047,0.007154,0.0045,-0.003645,-0.004709,0.000599,0.000297,-0.004542,-0.000543,0.01432,0.017732,0.006841,0.004525,0.0028 76,-0.003993,-0.001731,0.006902,0.01205,-0.000239

https://i.imgur.com/D7IrWAf.png

[Ayetooey]

..

Thanks, how does this work exactly? I'm distant from East Germany on the PCA.

https://i.postimg.cc/pX16vYFS/ayetooey.png

[Lemgrant]

Thanks, how does this work exactly? I'm distant from East Germany on the PCA.

https://i.postimg.cc/pX16vYFS/ayetooey.png

http://eurogenes.blogspot.com/2018/05/global25-past-compatible-datasheets.html

You are on your own. Between Bosnians/Serbians and English. This is how I see it.

[Blondie]

Wow great post. So our closest genetic brothers are Slovenians, Croats, Slovaks, Bohemians, Czechs, Austrians and East Germans. By the way what is "Scythian Hungary"? You mean jassic hungarians?

[Ford]

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Ford_scaled,0.134311,0.135065,0.051288,0.02261,0.0 30159,0.006136,0.005875,0.010846,0.00225,0.000547,-0.001461,-0.003747,0.007879,0.01101,-0.014794,0.006232,0.010561,-0.00076,0.006159,0.005628,-0.005116,-0.005812,0.004437,0.00241,-0.001078

Can you plot me?

[Gründig]

On the tree cluster, I plot right above Germany.

[J. Ketch]

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Ford_scaled,0.134311,0.135065,0.051288,0.02261,0.0 30159,0.006136,0.005875,0.010846,0.00225,0.000547,-0.001461,-0.003747,0.007879,0.01101,-0.014794,0.006232,0.010561,-0.00076,0.006159,0.005628,-0.005116,-0.005812,0.004437,0.00241,-0.001078

Can you plot me?
You're in the Croatian and Moldovan clusters.

https://i.postimg.cc/nzVrt2gT/ford.png

btw, if people are fully of one ethnicity ancestrally (at least 7/8 genealogically), I can add them as references for the clusters and make them more accurate.

[J. Ketch]

Wow great post. So our closest genetic brothers are Slovenians, Croats, Slovaks, Bohemians, Czechs, Austrians and East Germans. By the way what is "Scythian Hungary"? You mean jassic hungarians?
They're Scythian remains found in Hungary apparently. Some plot in the Balkans, others with Germans, so they were mixed. Definitely not Scythians straight from the Steppe.

[J. Ketch]

I already know where I'm on this PCA. How about doing some clustering in PAST3 program? This is something that Davidski hasn't done for me.
https://i.imgur.com/BSChu8g.png

http://eurogenes.blogspot.com/2018/05/global25-past-compatible-datasheets.html
Here's mine if you wouldn't mind doing it. I don't really understand those trees.

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
jketch_scaled,0.12862,0.138112,0.067882,0.050711,0 .039084,0.022311,0.004935,0.007615,0.003477,0.0020 05,-0.011854,0.008542,-0.015758,-0.013212,0.019679,-0.001193,-0.02021,0.004434,0.001383,-0.004877,0.004991,0.005441,-0.000986,0.011929,-0.003592

[karakartal]

Same as the other thread, give me your scaled coordinates and I'll put you in if you plot within the European variation.

https://i.postimg.cc/bwD1t1F4/NWEuro1.png
https://i.postimg.cc/YSBLLZFm/East-Euro1.png

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
TG_scaled,0.117238,0.108662,0.003017,-0.016473,0.004308,-0.011713,0.004935,0.002308,-0.008181,0.00492,-0.000487,0.002997,0.004311,0.000413,-0.009365,0.013657,0.02021,0,-0.001383,0.003877,-0.010606,0.000742,0.001602,-0.001446,0.001676

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
TG,0.0103,0.0107,0.0008,-0.0051,0.0014,-0.0042,0.0021,0.001,-0.004,0.0027,-0.0003,0.002,0.0029,0.0003,-0.0069,0.0103,0.0155,0,-0.0011,0.0031,-0.0085,0.0006,0.0013,-0.0012,0.0014

Can you please add me this plot?

[Stefanos.tasidis]

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Ford_scaled,0.134311,0.135065,0.051288,0.02261,0.0 30159,0.006136,0.005875,0.010846,0.00225,0.000547,-0.001461,-0.003747,0.007879,0.01101,-0.014794,0.006232,0.010561,-0.00076,0.006159,0.005628,-0.005116,-0.005812,0.004437,0.00241,-0.001078

Can you plot me?

first of all, where do you get all that gibberish from :D ?
second, how do you PCA ? I asked another member before and i was ignored.

[Lemgrant]

Here's mine if you wouldn't mind doing it. I don't really understand those trees.

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
jketch_scaled,0.12862,0.138112,0.067882,0.050711,0 .039084,0.022311,0.004935,0.007615,0.003477,0.0020 05,-0.011854,0.008542,-0.015758,-0.013212,0.019679,-0.001193,-0.02021,0.004434,0.001383,-0.004877,0.004991,0.005441,-0.000986,0.011929,-0.003592

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

[J. Ketch]

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
TG_scaled,0.117238,0.108662,0.003017,-0.016473,0.004308,-0.011713,0.004935,0.002308,-0.008181,0.00492,-0.000487,0.002997,0.004311,0.000413,-0.009365,0.013657,0.02021,0,-0.001383,0.003877,-0.010606,0.000742,0.001602,-0.001446,0.001676

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
TG,0.0103,0.0107,0.0008,-0.0051,0.0014,-0.0042,0.0021,0.001,-0.004,0.0027,-0.0003,0.002,0.0029,0.0003,-0.0069,0.0103,0.0155,0,-0.0011,0.0031,-0.0085,0.0006,0.0013,-0.0012,0.0014

Can you please add me this plot?
https://i.postimg.cc/NMYJZS0z/karakartal.png

In the West Eurasian ancient PCA
https://i.postimg.cc/90kBXnWV/karakartal2.png

[Blondie]

They're Scythian remains found in Hungary apparently. Some plot in the Balkans, others with Germans, so they were mixed. Definitely not Scythians straight from the Steppe.

I'm not surprised, scythians were iranic peoples and early hungarians had iranic genetic, plus jassic hungarians are descedants of scythians, sarmatians.

[Grace O'Malley]

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

Could you plot me on the tree when you have a chance? Thanks.

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Grace_scaled,0.138864,0.136081,0.064488,0.052003,0 .036314,0.017291,0.001645,0.006231,0.004909,-0.00328,-0.009094,0.004646,-0.011298,-0.009771,0.029994,0.005701,-0.007041,-0.004434,0.000377,0.007879,0.007112,0.007296,-0.005793,0.010845,-0.000479

[Lemgrant]

Could you plot me on the tree when you have a chance? Thanks.

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Grace_scaled,0.138864,0.136081,0.064488,0.052003,0 .036314,0.017291,0.001645,0.006231,0.004909,-0.00328,-0.009094,0.004646,-0.011298,-0.009771,0.029994,0.005701,-0.007041,-0.004434,0.000377,0.007879,0.007112,0.007296,-0.005793,0.010845,-0.000479

https://i.imgur.com/UXiq2sI.png

[Lemgrant]

.
https://i.imgur.com/oRAh8gm.png

[Cumansky]

https://i.imgur.com/oRAh8gm.png

Thanks, between Poland and Slovakia is accurate

My mother family they were Cossacks Zaporozhian they Slovakize their name later on but keep the root word Zaporozhian. My father family is Polish Szlachta

[Lemgrant]

Thank you.

Kaspias_scaled,0.103579,0.08632,0.013199,-0.010982,-0.002462,-0.009761,0.00094,0.005077,-0.006136,0.000911,0.000162,-0.000749,0.002379,-0.005505,-0.012486,0.013524,0.015255,0.00152,0.007668,0.0043 77,-0.004866,-0.000247,0,0.010001,-0.002155

https://i.imgur.com/SbY0KWd.png

[Ford]

Can you also put me on that tree?

Ford_scaled,0.134311,0.135065,0.051288,0.02261,0.0 30159,0.006136,0.005875,0.010846,0.00225,0.000547,-0.001461,-0.003747,0.007879,0.01101,-0.014794,0.006232,0.010561,-0.00076,0.006159,0.005628,-0.005116,-0.005812,0.004437,0.00241,-0.001078

[Lemgrant]

Can you also put me on that tree?

Ford_scaled,0.134311,0.135065,0.051288,0.02261,0.0 30159,0.006136,0.005875,0.010846,0.00225,0.000547,-0.001461,-0.003747,0.007879,0.01101,-0.014794,0.006232,0.010561,-0.00076,0.006159,0.005628,-0.005116,-0.005812,0.004437,0.00241,-0.001078

https://i.imgur.com/uAM6H4A.png

[Lemgrant]

Thanks, between Poland and Slovakia is accurate

My mother family they were Cossacks Zaporozhian they Slovakize their name later on but keep the root word Zaporozhian. My father family is Polish Szlachta

My result is accurate too. With little info that I have, my father is actually a Finno-Ugric Mordvin + Russian + something Finnic probably. While my mother is Ukrainian.

[Cumansky]

My result is accurate too. With little info that I have, my father is actually a Finno-Ugric Mordvin + Russian + something Finnic probably. While my mother is Ukrainian.

The other test you have some North Africa %?

[Lemgrant]

The other test you have some North Africa %?

haha I don't know. That is the only calc where I score something African.

[Cumansky]

haha I don't know. That is the only calc where I score something African.

That is the reason you close to Slovakia

Slovakia is highest in northern Europe for that blood

[Kaspias]

https://i.imgur.com/SbY0KWd.png

Thank you mate. Interestingly G25 overestimated my Central Asia and shifted me to the directly Turks. It is cool though. But i don't think it is accurate for myself when consider i clustered in same meta group with Caucasians and Iranians, even with Roma.

[Lemgrant]

VangosH_scaled,0.114961,0.148267,0.01697,-0.022287,0.020311,-0.00502,0.00329,0.005307,0.001227,0.007289,0.00568 4,0.000899,0.000297,0.01156,-0.010858,-0.012994,-0.004955,0.000253,0.008925,-0.01113,-0.005989,-0.003462,0.009244,-0.003374,-0.000479

Much appreciate it!

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

[Lemgrant]

Thank you mate. Interestingly G25 overestimated my Central Asia and shifted me to the directly Turks. It is cool though. But i don't think it is accurate for myself when consider i clustered in same meta group with Caucasians and Iranians, even with Roma.

That is with the Euclidean similarity index. There are many other methods. For example if I select the Cosine, then you cluster with Bulgarians.

https://i.imgur.com/MFfD3BM.png
https://i.imgur.com/vHKUwqT.png

[Kaspias]

That is with the Euclidean similarity index. There are many other methods. For example if I select the Cosine, then you cluster with Bulgarians.

https://i.imgur.com/MFfD3BM.png
https://i.imgur.com/vHKUwqT.png

Yeah, this one seems more accurate for me.

[Lemgrant]

Yeah, this one seems more accurate for me.

and if I select the Correlation Similarity Index, then you cluster with Greeks/Albanians.
https://i.imgur.com/KBPXFxj.png

[J. Ketch]

FilhoV

https://i.postimg.cc/FFnFHK60/filhov.png
https://i.postimg.cc/WzqB3sD7/filho2.png

[Lemgrant]

FilhoV
https://i.imgur.com/JPp5I4Y.png


for others, here is tutorial how to do it, it is very easy, so do it yourself
http://eurogenes.blogspot.com/2018/05/global25-past-compatible-datasheets.html

[FilhoV]

FilhoV
https://i.imgur.com/JPp5I4Y.png


for others, here is tutorial how to do it, it is very easy, so do it yourself
http://eurogenes.blogspot.com/2018/05/global25-past-compatible-datasheets.html

Thanks man I appreciate it, looks like I’m Southern Shifted compared to other Iberian populations hence the plot near the Canary Islands i’m actually even more so than shifted then the Canary Islanders which makes sense considering all my tests I took the Ethnogene test should get the results this week I’ll post it when it comes

[TheMaestro]

Where can i find g25 what is this calc

[Lemgrant]

Where can i find g25 what is this calc

$12 USD for G25 coordinates
http://bga101.blogspot.com/2018/02/the-powerful-global-25-now-available.html

[TheMaestro]

$12 USD for G25 coordinates
http://bga101.blogspot.com/2018/02/the-powerful-global-25-now-available.html

Oh, fuck it d00d then.

[Lemgrant]

Thanks man I appreciate it, looks like I’m Southern Shifted compared to other Iberian populations hence the plot near the Canary Islands i’m actually even more so than shifted then the Canary Islanders which makes sense considering all my tests I took the Ethnogene test should get the results this week I’ll post it when it comes

Portuguese cluster with Spanish_Canarias without your coordinates. You just replaced the Portuguese on that tree.

[FilhoV]

Portuguese cluster with Spanish_Canarias without your coordinates. You just replaced the Portuguese on that tree.

Thanks that’s interesting.

[Brás Garcia de Mascarenhas]

Are you still doing these?

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Viriato_scaled,0.105855,0.144205,0.034318,-0.003553,0.040315,-0.004741,-0.003995,0.006,0.024134,0.028064,-0.00747,0.007943,-0.011893,-0.008257,0.008822,-0.009944,-0.013951,-0.003167,-0.000126,-0.007003,-0.001622,-0.010016,0.004314,-0.008314,0.002395

[Vasconcelos]

If all you're doing is using modern samples, then you should definitely opt for unscaled coordinates, rather than scaled. Ger Huijbregts, who created nMonte, explained why a few months ago



The idea behind scaling is that multiplying PCA scores by the root of the eigenvalues results in PCA scores with distances that better represent the original data.

An obvious reason to distrust this idea is that the raw DNA data are not in a continuous format but categorical (SNP on a certain position). SmartPCA converts these categorical data into a PCA in continuous data.
I think the idea that post-SmartPCA distances should be adapted to pre-SmartPCA distances is preposterous.
Moreover the nature of eigenvalues is misunderstood. In the Global25 data the eigenvalues are largely determined by the sampling density, which is an interference
in the calculations, which should not be further enhanced.
The scaling is implemented in an amateurish way. Before the multiplication, the scores should have been centered (subtracting the mean).
From modern data science we can learn that most algorithms with multivariate data perform poorly when the variables have different variances. Therefore a standard way to make statistical calculations more robust is the normalizing of the data, i.e. dividing the variables by their standard deviation.
Scaling does the reverse. Ouch.

Sometimes a bad idea has unintended beneficial consequences, even scaling.
What many people don't realize, is that scaling penalizes the higher dimensions. (because the higher diemnsions have by definition smaller eigenvalues).
See the next plot of the standard deviation in the unscaled(green) and scaled(red) data.

https://i.postimg.cc/4sTSxm6C/scaled-vs-unscaled.jpg

Note the logarithmic vertical scale.
So scaling strongly penalizes the higher dimensions. After dimension 10 the scaled higher dimensions contribute virtually nothing to the distance.
Now this may in some cases be beneficial.
The many samples and the many dimensions make Global25 a great dataset.
But because it has so much detail to select from, there is a considerable risk that oddball admixtures percolate in the results, a.k.a. overfitting.
IMO this penalizing of the higher dimensions is why in some cases the scaled result appears more plausible than the unscaled result (with pen=0).
But scaling penalizes the higher dimensions too strongly (again the vertical scale on plot is logarithmic).
Also scaling uses the eigenvalues for another purpose and their side effect on the overfitting is not optimal. The nMonte3 way of slightly penalizing the greater distances is much better tailored to the task.



What all of us have in common is the understanding that working with unscaled data will sooner or later run you into trouble.
Where we differ, is the solution that we propose.
At the start of this longtime controversy is the assertion that pairwise distances of ancient populations from Global10 are inconsistent.
Someone proposed a simplistic transformation to repair this by multiplying the PCA scores with the eigenvalues.
That transformation failed to repair the inconsistencies. I commented that at least he should have multiplied with the square root of the eigenvalues. This is how I became the grumbling coauthor of a method that I don't believe in.
But even with the square root the method is still so amateurish that is should not pass the peer review of academic journals.
Moreover in the modern data science there are countless methods to regulate the overfitting of multivariate data.
I think that the slight penalization of greater distances in nMonte3 is in line with the regularization in modern data science.

I suppose that the better performance with ancient data is the main reason that Davidski adheres to scaled data.
However this better perfomance can easily be explained.
The Global25 dataset is dominated by modern samples and so is the Global25 PCA. So ancient data are mismatched in the Global25 PCA.
This difference between ancient and modern data is a result of modern changes in the population genetics. Which are less omnipresent than the ancient substrates.
So the recent changes in modern DNA have a higher probability of ending up in the higher dimensions of the PCA. The ancient populations are mainly represented in the lower dimensions, for them the higher dimensions are misfitted noise.
As shown in the plot of my previous post, the scaling transformation drastically reduces the higher dimension and keeps the lower dimensions.
So when fitting ancient populations with nMonte, scaled models will do better than unscaled (unless you penalize with nMonte3, but even than the fact remains that in the Global25 PCA ancient populations are undersampled).

But seriously, I have an advice for you.
You are mainly interested in your relation with modern NW-European populations.
In that case even proponents of the scaled method should admit that the main differences between these populations are in the higher dimensions.
And in that case the unscaled method is methodologically superior to the scaled method.


TLDR: Use scaled coordinates, especially if you're dealing with modern pops

[J. Ketch]

Are you still doing these?

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Viriato_scaled,0.105855,0.144205,0.034318,-0.003553,0.040315,-0.004741,-0.003995,0.006,0.024134,0.028064,-0.00747,0.007943,-0.011893,-0.008257,0.008822,-0.009944,-0.013951,-0.003167,-0.000126,-0.007003,-0.001622,-0.010016,0.004314,-0.008314,0.002395
https://i.postimg.cc/t4DwQn2K/viriato.png
https://i.postimg.cc/rpBvQXhs/viriato2.png

Are you fully Portuguese?

[J. Ketch]

If all you're doing is using modern samples, then you should definitely opt for unscaled coordinates, rather than scaled. Ger Huijbregts, who created nMonte, explained why a few months ago





TLDR: Use scaled coordinates, especially if you're dealing with modern pops
Is there an unscaled spreadsheet?

[Vasconcelos]

Is there an unscaled spreadsheet?

The dataset is avaliable at Eurogenes (https://drive.google.com/file/d/1Dj8ysMY4oePcbW5PszuiCnDBJi9ANjtt/view)

[firemonkey]

Tim_G_scaled,0.129758,0.131003,0.064865,0.047158,0 .043393,0.019243,0.002585,0.003,0.006954,-0.000547,-0.002598,0.005095,-0.010406,-0.011147,0.027823,0.006364,-0.021253,0.005828,0.001885,0.001751,0.004367,0.001 855,-0.002218,0.008555,-0.003113

[firemonkey]

Could you please do mine.

[J. Ketch]

Could you please do mine.
I already plotted you in the Northern Euro PCA, hardly going to be much difference.

https://i.postimg.cc/HL5dzPq4/firemonkey.png

[Stefanos.tasidis]

does anyone know how to open a .dat file ? i'm running macOS here

[J. Ketch]

does anyone know how to open a .dat file ? i'm running macOS here
There's your first mistake.

[Stefanos.tasidis]

There's your first mistake.

dont worry about my mistakes :D
can i open it here at all ?

[J. Ketch]

dont worry about my mistakes :D
can i open it here at all ?
I don't know, sorry.

[Brás Garcia de Mascarenhas]

https://i.postimg.cc/t4DwQn2K/viriato.png
https://i.postimg.cc/rpBvQXhs/viriato2.png

Are you fully Portuguese?

Thank you and yes, I am fully Portuguese.

[Stefanos.tasidis]

I don't know, sorry.

all good, thanks though

[Peterski]

Please add me:


PeterskiLD_scaled,0.135449,0.142174,0.065619,0.056 848,0.036007,0.021475,0.004935,0.006,0.005522,-0.01877,-0.004709,-0.005245,0.011744,0.011698,-0.005157,0.00053,0.002868,0.000887,-0.003897,-0.003252,-0.009358,-0.001978,0.007025,0.015785,-0.002634

[J. Ketch]

Please add me:


PeterskiLD_scaled,0.135449,0.142174,0.065619,0.056 848,0.036007,0.021475,0.004935,0.006,0.005522,-0.01877,-0.004709,-0.005245,0.011744,0.011698,-0.005157,0.00053,0.002868,0.000887,-0.003897,-0.003252,-0.009358,-0.001978,0.007025,0.015785,-0.002634
https://i.postimg.cc/yYHRHmyG/peterski.png

[Gründig]

Could you plot me?


Gründig_scaled,0.122929,0.140143,0.054305,0.030685 ,0.032621,0.014502,0.0094,0.008307,0,-0.000182,-0.003573,0.006894,-0.013082,0.001376,0.007736,0.002917,-0.002477,0.004054,-0.001257,0.001626,0.006239,0.007419,-0.001849,0.014339,0.007903

[J. Ketch]

Could you plot me?


Gründig_scaled,0.122929,0.140143,0.054305,0.030685 ,0.032621,0.014502,0.0094,0.008307,0,-0.000182,-0.003573,0.006894,-0.013082,0.001376,0.007736,0.002917,-0.002477,0.004054,-0.001257,0.001626,0.006239,0.007419,-0.001849,0.014339,0.007903
https://i.postimg.cc/mrP3mB67/grundig.png

In the German, French East and Dutch clusters.

[J. Ketch]

Pedro Ruben
https://i.postimg.cc/L4062XmP/pedroruben.png
https://i.postimg.cc/0NBPxXss/pedroruben2.png

[Thracian]

Pedro Ruben
https://i.postimg.cc/L4062XmP/pedroruben.png
https://i.postimg.cc/0NBPxXss/pedroruben2.png

Could you also add me if you have time?

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Thracian_scaled,0.112685,0.114755,0.00264,-0.006137,0.00677,0,0.004465,0,-0.001841,0.002734,0.001299,-0.001948,-0.00223,0.002477,-0.006515,0.009016,0.013038,0.00228,0.006034,0.0057 53,-0.004492,0.00507,-0.000739,0.002048,-0.001317

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Thracian,0.0099,0.0113,0.0007,-0.0019,0.0022,0,0.0019,0,-0.0009,0.0015,0.0008,-0.0013,-0.0015,0.0018,-0.0048,0.0068,0.01,0.0018,0.0048,0.0046,-0.0036,0.0041,-0.0006,0.0017,-0.0011

Thanks in advance.

[J. Ketch]

Could you also add me if you have time?

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Thracian_scaled,0.112685,0.114755,0.00264,-0.006137,0.00677,0,0.004465,0,-0.001841,0.002734,0.001299,-0.001948,-0.00223,0.002477,-0.006515,0.009016,0.013038,0.00228,0.006034,0.0057 53,-0.004492,0.00507,-0.000739,0.002048,-0.001317

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Thracian,0.0099,0.0113,0.0007,-0.0019,0.0022,0,0.0019,0,-0.0009,0.0015,0.0008,-0.0013,-0.0015,0.0018,-0.0048,0.0068,0.01,0.0018,0.0048,0.0046,-0.0036,0.0041,-0.0006,0.0017,-0.0011

Thanks in advance.
https://i.postimg.cc/3xYCX7ct/thracian.png

West Eurasian plot is better for you.

https://i.postimg.cc/YCCL2SVB/thracian2.png

[Defski]

Could you also add me if you have time?

,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Defski_scaled,0.110408,0.144205,0.036204,-0.000323,0.037545,0.000279,0.000705,-0.000923,0.023725,0.033531,-0.005846,0.001349,-0.006095,-0.023121,0.0038,0.00769, 0.000782,0.00228,-0.009553,-0.004127,0.002995,-0.007543,-0.000986,-0.008073,-0.002634


,PC1,PC2,PC3,PC4,PC5,PC6,PC7,PC8,PC9,PC10,PC11,PC1 2,PC13,PC14,PC15,PC16,PC17,PC18,PC19,PC20,PC21,PC2 2,PC23,PC24,PC25
Defski,0.0097,0.0142,0.0096,-0.0001,0.0122,0.0001,0.0003,-0.0004,0.0116,0.0184,-0.0036,0.0009,-0.0041,-0.0168,0.0028,0.0058,0.0006,0.0018,-0.0076,-0.0033,0.0024,-0.0061, -0.0008,-0.0067,-0.0022

Thank you

[Nurzat]

...

if you still have that tree available, can you add me, I am curious where I fall on (since I'm a bit mixed) - probably with northeast/northwest Balkanites (Moldovans and Yugoslavs)


Nurzat,0.12520541921179,0.12897223615957,0.0460087 217818535,0.0268091284826643,0.027697490861087,0.0 117134077022872,0.00775535105588393,0.007615067301 08145,-0.00347690523310602,-0.000182236110581849,-0.00893136327779808,-0.0040463983985762,0.00416249924924918,0.010184077 7687526,-0.0126219879575287,0.00291697103173823,0.004693825 73174591,0.00139357454052519,0.00175977271259671,-0.00537757938109704,-0.0101071642907395,-0.00296766574937273,0.00628563361961227,-0.00144598755181364,-0.00742448382044166


a model I tried for those who posted their G25 on here:

https://scontent.fotp1-1.fna.fbcdn.net/v/t1.0-9/75456729_124034205703045_7616258844502523904_n.jpg ?_nc_cat=107&_nc_oc=AQnGNEVAYD57APbrHZfNZgApcm9xW5db73Sd9OLXD8t mkDenzVOhBLCR9Rd8mNjl2Ms&_nc_ht=scontent.fotp1-1.fna&oh=1d4aec45aea2ec175d36247330c16cbb&oe=5E5A6D11

https://scontent.fotp1-1.fna.fbcdn.net/v/t1.0-9/74614154_124040502369082_5637521631178915840_n.jpg ?_nc_cat=110&_nc_oc=AQnSu4DnsFli5Fb-qrGbSS-TafTmCb1M8y_wGRm6yi3W6EuO_9y1OXWbij859Tq87tM&_nc_ht=scontent.fotp1-1.fna&oh=d334fe696befc8323d8cfc242cd04925&oe=5E5B23B3

[Lemgrant]

if you still have that tree available, can you add me, I am curious where I fall on (since I'm a bit mixed) - probably with northeast/northwest Balkanites (Moldovans and Yugoslavs)


Nurzat,0.12520541921179,0.12897223615957,0.0460087 217818535,0.0268091284826643,0.027697490861087,0.0 117134077022872,0.00775535105588393,0.007615067301 08145,-0.00347690523310602,-0.000182236110581849,-0.00893136327779808,-0.0040463983985762,0.00416249924924918,0.010184077 7687526,-0.0126219879575287,0.00291697103173823,0.004693825 73174591,0.00139357454052519,0.00175977271259671,-0.00537757938109704,-0.0101071642907395,-0.00296766574937273,0.00628563361961227,-0.00144598755181364,-0.00742448382044166


with Euclidean similarity index:
https://i.imgur.com/R6lszeC.png

and you on PCA:
https://i.imgur.com/3wjJX2d.png
https://lemgrant.github.io/g25views/