GEO datasets

[lsand039]

For 20 variables: 1 hr runs created the same graphs; score: -2676.6239

I will post updates for other variables as scores match/ run times reach the 8 hour mark.

[lsand039]

For all the variables (11275):
1 hr runs scores:-1628660.0213, -1632413.0334, -1633496.9970
2 hr runs Scores: -1590897.7545, -1596287.0363, -1597454.9918
4 hr runs Scores: -1531627.7215, -1534956.1270, -1536426.1266
8 hr runs Scores: -1490300.5325, -1490740.5118, -1492964.8043

For 50 variables:
1 hr runs scores: -4791.2054, -4799.2916, -4800.4300
2 hr runs Scores: -4796.3688, -4799.1864 , -4800.9698 (I had to increase the number of restarts from 10,000 to 100,000 so it wouldn't run out for the 4 hr run.)
4 hr runs Scores: -4793.6639, -4795.3173, -4796.3005
8 hr runs scores: -4788.3943, -4795.4177, -4797.8694

[lsand039]

Here are the log scores with their times and the path used to run Banjo:

50 variables: Total score -4788.32851422004
8 hr p3: Log score -4788.3943 is 93.633142376511 % of total score
1 hr p4: Log score -4791.2054 is 5.63098513281088 % of total score
4 hr p4: Log score -4793.6639 is 0.481805104616638 % of total score
4 hr p2: Log score -4795.3173 is 0.0922165564065525 % of total score
8 hr p2: Log score -4795.4177 is 0.0834076210771201 % of total score
4 hr p3: Log score -4796.3005 is 0.0344993224602483 % of total score
2 hr p2: Log score -4796.3688 is 0.0322216853840715 % of total score
8 hr p4: Log score -4797.8694 is 0.00718531733598712 % of total score
2 hr p4: Log score -4799.1864 is 0.00192521891819581 % of total score
1 hr p2: Log score -4799.2916 is 0.00173297517370219 % of total score
1 hr p3: Log score -4800.4300 is 0.000555125916168481 % of total score
2 hr p3: Log score -4800.9698 is 0.000323563363696739 % of total score



100 variables: Total score -8405.6847794181
4 hr p2: Log score -8405.6848 is 99.9979418312144 % of total score
2 hr p3: Log score -8416.6095 is 0.00180075295014171 % of total score
8 hr p3: Log score -8418.8043 is 0.000200569368016131 % of total score
4 hr p4: Log score -8420.0688 is 5.66368686121385e-05 % of total score
4 hr p3: Log score -8425.8161 is 1.80750104834464e-07 % of total score
2 hr p4: Log score -8428.2728 is 1.54934203621032e-08 % of total score
1 hr p4: Log score -8428.6218 is 1.09289522878104e-08 % of total score
3 hr p2: Log score -8430.6565 is 1.42862928273984e-09 % of total score
1 hr p3: Log score -8431.4786 is 6.2789359664406e-10 % of total score
8 hr p4: Log score -8432.1701 is 3.14464351520163e-10 % of total score
1 hr p2: Log score -8438.0204 is 9.05353974254347e-13 % of total score
2 hr p2: Log score -8446.4187 is 2.03930913665084e-16 % of total score



250 variables: Total score -19834.2229
8 hr p4: Log score -19834.2229 is 99.9999999989086 % of total score
8 hr p3: Log score -19859.5217 is 1.03007954037305e-09 % of total score
4 hr p3: Log score -19886.0362 is 3.14607970245965e-21 % of total score
2 hr p4: Log score -19896.6237 is 7.93737490284349e-26 % of total score
2 hr p3: Log score -19902.7158 is 1.79436785466255e-28 % of total score
4 hr p4: Log score -19919.6716 is 7.76427848768085e-36 % of total score
8 hr p2: Log score -19926.0018 is 1.38334394932154e-38 % of total score
1 hr p4: Log score -19931.0756 is 8.65778571467393e-41 % of total score
4 hr p2: Log score -19943.7168 is 2.80158257734128e-46 % of total score
1 hr p3: Log score -19960.0288 is 2.30776636379193e-53 % of total score
2 hr p2: Log score -19968.3238 is 5.7639354925715e-57 % of total score
1 hr p2: Log score -19983.2777 is 1.84638753180575e-63 % of total score



500 variables: Total score -40839.0892
4 hr p2: Log score -40839.0892 is 100 % of total score
1 hr p2: Log score -40874.4861 is 4.23956846908447e-14 % of total score
4 hr p4: Log score -40925.1183 is 4.34546830785659e-36 % of total score
2 hr p2: Log score -40933.6435 is 8.62162779136965e-40 % of total score
2 hr p4: Log score -40934.234 is 4.77681451912811e-40 % of total score
4 hr p3: Log score -40938.3582 is 7.72718083544599e-42 % of total score
8hr p3: Log score -40957.0374 is 5.96688392598214e-50 % of total score
8 hr p4: Log score -40958.6393 is 1.20240634415973e-50 % of total score
2 hr p2: Log score -40963.3388 is 1.09416883657224e-52 % of total score
1 hr p4: Log score -41036.3238 is 2.19837400285558e-84 % of total score
2 hr p3: Log score -41036.4825 is 1.87576766598699e-84 % of total score
1 hr p3: Log score -41039.9717 is 5.72583381557063e-86 % of total score


1000 variables: Total score -86177.8850
8 hr p2: Log score -86177.8850 is 100 % of total score
8 hr p4: Log score -86509.9770 is 5.94671213296462e-143 % of total score
4 hr p4: Log score -86543.7666 is 1.25788254321473e-157 % of total score
8 hr p3: Log score -86632.2137 is 4.87026530402326e-196 % of total score
1 hr p3: Log score -86682.7976 is 5.23894665810111e-218 % of total score
4 hour p2: Log score -86697.7434 is 1.69186423168301e-224 % of total score
4 hr p3: Log score -86707.4030 is 1.07957925725917e-228 % of total score
1 hr p3: Log score -86759.3201 is 3.06157205495037e-251 % of total score
1 hr p4: Log score -86764.9068 is 1.14728549553091e-253 % of total score
1 hr p2: Log score -86914.2270 is 1.62448784352602e-318 % of total score
2 hr p2: Log score -86919.3822 is 9.38724727098368e-321 % of total score
1 hr p4: Log score -87009.2853 is 0 % of total score




2500 variables: Total score -246895.568770766
4 hr p3: Log score -246896.1231 is 57.4457458557984 % of total score
8 hr p2: Log score -246896.5109 is 38.9796982168129 % of total score
8 hr p4: Log score -246898.9001 is 3.57455592641719 % of total score
4 hr p4: Log score -247010.185 is 1.67033702218447e-48 % of total score
4 hr p2: Log score -247268.1052 is 1.61988608860976e-160 % of total score
8 hr p3: Log score -247354.9949 is 2.97692046407544e-198 % of total score
1 hr p3: Log score -247500.2865 is 2.36824748427471e-261 % of total score
1 hr p4: Log score -247729.8162 is 0 % of total score
2 hr p4: Log score -247805.2454 is 0 % of total score
2 hr p3: Log score -247831.6911 is 0 % of total score
2 hr p2: Log score -248075.5014 is 0 % of total score
1 hr p2: Log score -248443.7865 is 0 % of total score



5000 variables: Total score -562655.0164
8 hr p2: Log score -562655.0164 is 100 % of total score
8 hr p4: Log score -563009.3653 is 1.28300415111069e-152 % of total score
4 hr p3: Log score -563435.5581 is 0 % of total score
4 hr p4: Log score -564038.9697 is 0 % of total score
8 hr p3: Log score -564505.7211 is 0 % of total score
2 hr p4: Log score -565709.3191 is 0 % of total score
2 hr p3: Log score -566119.8419 is 0 % of total score
4 hr p2: Log score -566426.1175 is 0 % of total score
2 hr p2: Log score -567301.601 is 0 % of total score
1 hr p4: Log score -573509.7450 is 0 % of total score
1 hr p3: Log score -573915.3555 is 0 % of total score
1 hr p2: Log score -574401.1203 is 0 % of total score


11275 variables: Total score -1490300.5325
8 hr p3: Log score -1490300.5325 is 100 % of total score
8 hr p4: Log score -1490740.5118 is 8.30649596309217e-190 % of total score
8 hr p2: Log score -1492964.8043 is 0 % of total score
4 hr p4: Log score -1531627.7215 is 0 % of total score
4 hr p3: Log score -1534956.1270 is 0 % of total score
4 hr p2: Log score -1536426.1266 is 0 % of total score
2 hr p4: Log score -1590897.7545 is 0 % of total score
2 hr p2: Log score -1596287.0363 is 0 % of total score
2 hr p3: Log score -1597454.9918 is 0 % of total score
1 hr p4: Log score -1628660.0213 is 0 % of total score
1 hr p2: Log score -1632413.0334 is 0 % of total score
1 hr p3: Log score -1633496.9970 is 0 % of total score

[shstyoo]

I was asked to look back at the code and the data to double check if everything ran properly. It looks as though everything is working as intended (did some QA on my script, and it seems to be working fine). There was a concern I read in an earlier post about the script returning a black output? Can you elaborate on that, if you haven't already conglomerated those 4 files?

It also seems that Banjo isn't able to run with such a large filesize. Have you been able to solve that issue? Asides from messing around with the settings in Banjo?

[lsand039]

I thought I would be able to create file that only matched the common genes of all 4 files with the probe IDs of the original files using the script. I realized that the files I posted earlier that led to the blank script was my own misunderstanding on how the script worked, and making new keys that matched the common genes to probe IDs would be more time consuming than if I used Excel to eliminate the uncommon genes.

I was only able to run large files Banjo by adjusting the settings to cache fastLevel1, precomputeLogGamma no, and Proposer RandomLocalMove. Cache fastLevel2, precomputeLogGamma yes, and Proposer AllLocalMoves required too much memory for Banjo to run on files with as many variables as we had. Would results change significantly if we could apply those settings on the data?

[lsand039]

Here are the overall, 1st and 2nd degree Markov Blanket graphs for 20, 50, and 100 variables.

Color codes:

1st degree MB:
Lavender- Alzheimer node
Pink- Parents of Alzheimer node
Yellow- Children of Alzheimer node
Orange- Other Parents of Alzheimer children

Green- all 2nd degree MB nodes

[lsand039]

The rest of the graphs:

[lsand039]

The graphs for 250 variables:

[lsand039]

Here are the arcs denoting influence score strengths for 20 variables. The thicker the arc, the larger the score. Blue arcs show positive scores, red arcs show negative scores, and black arcs have a score of 0 or did not have an influence score.

[lsand039]

Here are the arcs denoting influence score strengths for 50 variables.