GEO datasets

[lsand039]

Here are the loglikelihoods for the Y-structures created from the clinical variables and APOE, APP, PSEN1, and PSEN2

[cwyoo]

Here are the loglikelihoods for the Y-structures created from the clinical variables and APOE, APP, PSEN1, and PSEN2

Great.

I am assuming you calculated Y structure in diagram (a). Could you also calculate Y structure in diagram (b) and (c) as well? Also report the normalized score by same clinical variables and genes together, e.g.,

normalize these nine:
from diagram (a)
Age & BR APOE → PSEN1 -5288.0901
Age & BR APOE 0 PSEN1 -5290.3499
Age & BR APOE ← PSEN1 -5321.0178
from diagram (b)
Age & BR APOE → PSEN1 u
Age & BR APOE 0 PSEN1 v
Age & BR APOE ← PSEN1 w
from diagram (c)
Age & BR APOE → PSEN1 x
Age & BR APOE 0 PSEN1 y
Age & BR APOE ← PSEN1 z


normalize these nine:
from diagram (a)
Age & BR APP → PSEN1 -5323.0673
Age & BR APP 0 PSEN1 -5348.2651
Age & BR APP ← PSEN1 -5362.7729
from diagram (b)
Age & BR APP → PSEN1 a
Age & BR APP 0 PSEN1 b
Age & BR APP ← PSEN1 c
from diagram (c)
Age & BR APP → PSEN1 d
Age & BR APP 0 PSEN1 e
Age & BR APP ← PSEN1 f

etc.

[cwyoo]

Here are the loglikelihoods for the Y-structures created from the clinical variables and APOE, APP, PSEN1, and PSEN2

Great.

I am assuming you calculated Y structure in diagram (a). Could you also calculate Y structure in diagram (b) and (c) as well? Also report the normalized score by same clinical variables and genes together, e.g.,

normalize these nine:
from diagram (a)
Age & BR APOE → PSEN1 -5288.0901
Age & BR APOE 0 PSEN1 -5290.3499
Age & BR APOE ← PSEN1 -5321.0178
from diagram (b)
Age & BR APOE → PSEN1 u
Age & BR APOE 0 PSEN1 v
Age & BR APOE ← PSEN1 w
from diagram (c)
Age & BR APOE → PSEN1 x
Age & BR APOE 0 PSEN1 y
Age & BR APOE ← PSEN1 z


normalize these nine:
from diagram (a)
Age & BR APP → PSEN1 -5323.0673
Age & BR APP 0 PSEN1 -5348.2651
Age & BR APP ← PSEN1 -5362.7729
from diagram (b)
Age & BR APP → PSEN1 a
Age & BR APP 0 PSEN1 b
Age & BR APP ← PSEN1 c
from diagram (c)
Age & BR APP → PSEN1 d
Age & BR APP 0 PSEN1 e
Age & BR APP ← PSEN1 f

etc.

Also you can derive four different diagrams from (c) by removing one arc at a time (call them, (c1), (c2), (c3), (c4)) and report by normalizing 21 log probability scores from 7 diagrams, (a), (b), (c), (c1), (c2), (c3), and (c4).

[lsand039]

Here are the all the normalized Y structure scores. I'll be posting the images, output files, and setting files for the best structure for each set of variables in the upcoming posts.

[lsand039]

Best structure for AD, Age, APOE, and APOE (98.65%)

AD.Age.APOE.APP.png (28.32 KiB) Viewed 156919 times

Output files:

AD.Age.APOE.<-c4-.APP.static.report.2017.11.15.13.54.47.txt

(8.99 KiB) Downloaded 173 times

AD.Age.APOE.<-c4-.APP.graph.2017.11.15.13.54.47.txt

(349 Bytes) Downloaded 170 times

Input files:

AD.Age.APOE.APP.txt

data file

(17.63 KiB) Downloaded 178 times

settingsAD.Age.APOE.-c4-2.APP.txt

setting files

(5.86 KiB) Downloaded 176 times

[lsand039]

Best Structures for AD, Age, APOE, and PSEN1:

90.54%

AD.Age.APOE.PSEN1a.png (27.73 KiB) Viewed 156919 times

9.45%

AD.Age.APOE.PSEN1b.png (26.34 KiB) Viewed 156919 times

Files (90.54%):

AD.Age.APOE.->.PSEN1.graph.2017.11.14.09.40.18.txt

(340 Bytes) Downloaded 174 times

AD.Age.APOE.->.PSEN1.static.report.2017.11.14.09.40.18.txt

(8.88 KiB) Downloaded 171 times

settingsAD.Age.APOE.2.PSEN1.txt

Settings files

(5.89 KiB) Downloaded 186 times

Files (9.45%):

AD.Age.APOE.0.PSEN1.graph.2017.11.08.13.16.01.txt

(329 Bytes) Downloaded 181 times

AD.Age.APOE.0.PSEN1.static.report.2017.11.08.13.16.01.txt

(8.82 KiB) Downloaded 180 times

settingsAD.Age.APOE.0.PSEN1.txt

(5.85 KiB) Downloaded 165 times

Data file:

AD.Age.APOE.PSEN1.txt

(17.63 KiB) Downloaded 178 times

[lsand039]

The best structure for AD, Age, APOE, and PSEN1:

97.85%

AD.Age.APOE.PSEN2.png (26.04 KiB) Viewed 156919 times

Output files:

AD.Age.APOE.-c4-.PSEN2.graph.2017.11.15.11.44.03.txt

(342 Bytes) Downloaded 185 times

AD.Age.APOE.-c4-.PSEN2.static.report.2017.11.15.11.44.03.txt

(8.88 KiB) Downloaded 163 times

Input files:

AD.Age.APOE.PSEN2.txt

data file

(17.63 KiB) Downloaded 178 times

settingsAD.Age.APOE.-c4-.PSEN2.txt

(5.87 KiB) Downloaded 175 times

[lsand039]

Best Structure for AD, Age, APP, and PSEN1:

100%

AD.Age.APP.PSEN1.png (27.03 KiB) Viewed 156919 times

Output files:

AD.Age.APP.->.PSEN1.graph.2017.11.08.10.00.55.txt

(338 Bytes) Downloaded 181 times

AD.Age.APP.->.PSEN1.static.report.2017.11.08.10.00.55.txt

(8.93 KiB) Downloaded 167 times

Input files:

settingsAD.Age.APP.2.PSEN1.txt

(5.88 KiB) Downloaded 178 times

AD.Age.APP.PSEN1.txt

data file

(17.63 KiB) Downloaded 179 times

[lsand039]

Best Structures for AD, Age, APP, and PSEN2:

56.01%

AD.Age.APP.PSEN2a.png (26.39 KiB) Viewed 156919 times

34.83%

AD.Age.APP.PSEN2b.png (26.09 KiB) Viewed 156919 times

8.87%

AD.Age.APP.PSEN2c.png (26.1 KiB) Viewed 156919 times

Files (56.01%):

AD.Age.APP.-c0-.PSEN2.graph.2017.11.27.14.58.31.txt

(350 Bytes) Downloaded 176 times

AD.Age.APP.-c0-.PSEN2.static.report.2017.11.27.14.58.31.txt

(8.93 KiB) Downloaded 173 times

Files (34.83%):

AD.Age.APP.-c4-.PSEN2.graph.2017.11.22.08.20.08.txt

(340 Bytes) Downloaded 153 times

AD.Age.APP.-c4-.PSEN2.static.report.2017.11.22.08.20.08.txt

(8.88 KiB) Downloaded 176 times

Files (8.87%):

AD.Age.APP.-c1-.PSEN2.graph.2017.11.18.10.43.25.txt

(340 Bytes) Downloaded 167 times

AD.Age.APP.-c1-.PSEN2.static.report.2017.11.18.10.43.25.txt

(8.88 KiB) Downloaded 164 times

Datafile:

AD.Age.APP.PSEN2.txt

(17.63 KiB) Downloaded 174 times

[lsand039]

(continued from last post)
Settings:

settingsAD.Age.APP.-c0-.PSEN2.txt

56.01%

(5.86 KiB) Downloaded 162 times

settingsAD.Age.APP.-c4-.PSEN2.txt

34.83%

(5.86 KiB) Downloaded 154 times

settingsAD.Age.APP.-c1-.PSEN2.txt

8.87%

(5.86 KiB) Downloaded 149 times