I rework Zhenghua's script so that each BDE score can be analyzed. I also left the values in the negative format. BDE score 7 and 8 are the best network .
##### Rework
> bde=vector()
> bde[1] = -3792.715
> bde[2] = -3681.208
> bde[3] = -3630.236
> bde[4] = -3627.093
> bde[5] = -3615.076
> bde[6]= -3627.093
> bde[7] = -3603.086
> bde[8]= -3603.086
> bde[9]= -3621.687
>
> per1 =vector()
> for(i in 1:9){
+ per1[i] = exp(-log(sum(exp(bde-bde[i]))))
+ }
>
> per1
[1] 2.208718e-83 5.902217e-35 8.088602e-13 1.874395e-11
[5] 3.102972e-06 1.874395e-11 4.999984e-01 4.999984e-01
[9] 4.175005e-09
SMLG (Statistical Machine Learning Group) Discussion Forum
Changwon Yoo, S.M., Ph.D., PI
Zinc & Aging part II Genetic Data
33 posts
• Page 3 of 4 • 1, 2, 3, 4
Re: Zinc & Aging part II Genetic Data
by rpazo001 » Thu May 18, 2023 5:18 pm
- rpazo001
- Posts: 58
- Joined: Fri May 29, 2020 12:34 pm
Re: Zinc & Aging part II Genetic Data
by rpazo001 » Fri Jun 02, 2023 2:45 pm
> ##### Rework
> bde=vector()
> bde[1] = -3792.715 ###1000 restarts
> bde[2] = -3681.208 ###5000 restarts
> bde[3] = -3630.236 ###10000 restarts
> bde[4] = -3627.093 ###20000 restarts
> bde[5] = -3615.076 ###20000 restarts
> bde[6]= -3627.093 ###20000 restarts
> bde[7] = -3603.086 ###40000 restarts using best DAG from 20000
> bde[8]= -3603.086 ###40000 restarts using best DAG from 20000
> bde[9]= -3621.687 ###40000 restarts random DAG
> bde[10]= -3598.474 ####80000 restarts using best DAG from 40000
> bde[11]= -3596.369 ####80000 restarts using best DAG from 40000
> bde[12]= -3596.341 ###160000 restarts using best DAG from 40000
>
>
>
> per1 =vector()
> for(i in 1:12){
+ per1[i] = exp(-log(sum(exp(bde-bde[i]))))
+ }
>
>
> per1
[1] 2.483361e-86 6.636127e-38 9.094378e-16 2.107466e-14
[5] 3.488810e-09 2.107466e-14 5.621707e-04 5.621707e-04
[9] 4.694145e-12 5.660233e-02 4.645412e-01 4.777321e-01
> bde=vector()
> bde[1] = -3792.715 ###1000 restarts
> bde[2] = -3681.208 ###5000 restarts
> bde[3] = -3630.236 ###10000 restarts
> bde[4] = -3627.093 ###20000 restarts
> bde[5] = -3615.076 ###20000 restarts
> bde[6]= -3627.093 ###20000 restarts
> bde[7] = -3603.086 ###40000 restarts using best DAG from 20000
> bde[8]= -3603.086 ###40000 restarts using best DAG from 20000
> bde[9]= -3621.687 ###40000 restarts random DAG
> bde[10]= -3598.474 ####80000 restarts using best DAG from 40000
> bde[11]= -3596.369 ####80000 restarts using best DAG from 40000
> bde[12]= -3596.341 ###160000 restarts using best DAG from 40000
>
>
>
> per1 =vector()
> for(i in 1:12){
+ per1[i] = exp(-log(sum(exp(bde-bde[i]))))
+ }
>
>
> per1
[1] 2.483361e-86 6.636127e-38 9.094378e-16 2.107466e-14
[5] 3.488810e-09 2.107466e-14 5.621707e-04 5.621707e-04
[9] 4.694145e-12 5.660233e-02 4.645412e-01 4.777321e-01
- rpazo001
- Posts: 58
- Joined: Fri May 29, 2020 12:34 pm
Re: Zinc & Aging part II Genetic Data
by rpazo001 » Sat Jun 03, 2023 11:48 am
Pearson Correlation's
- Attachments
-
Pearson Correlations.docx- (19.57 KiB) Downloaded 33 times
- rpazo001
- Posts: 58
- Joined: Fri May 29, 2020 12:34 pm
Re: Zinc & Aging part II Genetic Data
by rpazo001 » Wed Jul 05, 2023 1:38 pm
Mouse dataset
- Attachments
-
- Mousedata.csv
- (89.5 KiB) Downloaded 29 times
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- Posts: 58
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Re: Zinc & Aging part II Genetic Data
by rpazo001 » Sun Jul 16, 2023 2:30 pm
Mouse network dot file
Mouse netfile
Mouse netfile
- Attachments
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- MouseBNtext.txt
- netfile
- (1.76 MiB) Downloaded 21 times
-
- dagmouse.dot
- (409.86 KiB) Downloaded 20 times
Last edited by rpazo001 on Thu Jul 27, 2023 11:22 am, edited 1 time in total.
- rpazo001
- Posts: 58
- Joined: Fri May 29, 2020 12:34 pm
Re: Zinc & Aging part II Genetic Data
by rpazo001 » Sun Jul 16, 2023 2:49 pm
Human network dot file, netfile, data
- Attachments
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- Humandata.csv
- human data
- (103.66 KiB) Downloaded 19 times
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- HumanBNtext.txt
- net file
- (136.65 KiB) Downloaded 23 times
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- daghuman.dot
- dotfile
- (66.04 KiB) Downloaded 19 times
Last edited by rpazo001 on Thu Jul 27, 2023 11:17 am, edited 2 times in total.
- rpazo001
- Posts: 58
- Joined: Fri May 29, 2020 12:34 pm
Re: Zinc & Aging part II Genetic Data
by rpazo001 » Sun Jul 16, 2023 3:04 pm
Rat network dot file
Rat network net file ( I had to save it as a text file to post)
Data for network
Rat network net file ( I had to save it as a text file to post)
Data for network
- Attachments
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- BNRAT textfile.txt
- net file
- (466.4 KiB) Downloaded 26 times
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- RATBNZ.csv
- data
- (16.54 KiB) Downloaded 22 times
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- dagrat.dot
- dot file
- (31.8 KiB) Downloaded 22 times
Last edited by rpazo001 on Thu Jul 27, 2023 8:14 am, edited 1 time in total.
- rpazo001
- Posts: 58
- Joined: Fri May 29, 2020 12:34 pm
Re: Zinc & Aging part II Genetic Data
by rpazo001 » Thu Jul 20, 2023 2:24 pm
Data for BANJO
- Attachments
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- BANJO12.csv
- (19.44 KiB) Downloaded 24 times
- rpazo001
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Re: Zinc & Aging part II Genetic Data
by samanthagonzales » Wed Aug 02, 2023 2:49 pm
Here are the unformatted networks for 3 independent 1-hour banjo runs on the BANJO12 data (552 mouse genes+fasting).
Fasting is highlighted in yellow - ctrl-F to find the node does not work in Firefox, but works in Edge and Chrome.
Fasting is highlighted in yellow - ctrl-F to find the node does not work in Firefox, but works in Edge and Chrome.
- Attachments
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- mouse500.r1.fasting.svg
- (1.59 MiB) Downloaded 20 times
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- mouse500.r2.fasting.svg
- (1.7 MiB) Downloaded 16 times
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- mouse500.r3.fasting.svg
- (1.62 MiB) Downloaded 21 times
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- mouse500_dot_files.zip
- dot graphs to generate figures
- (35.57 KiB) Downloaded 21 times
- samanthagonzales
- Posts: 41
- Joined: Wed Jun 07, 2023 2:38 pm
Re: Zinc & Aging part II Genetic Data
by samanthagonzales » Tue Aug 29, 2023 10:48 am
The mouse representative network (roughly 30 genes) -
I used the genes from (1) the MB of fasting, (2) the genes of interest (3) top 10 genes with highest probabilities 'finalmouseprobs8_8' and (4) the MB of the top 10 genes.
I used the genes from (1) the MB of fasting, (2) the genes of interest (3) top 10 genes with highest probabilities 'finalmouseprobs8_8' and (4) the MB of the top 10 genes.
- Attachments
-
- image file for mouse representative network
- mouse_representative_network.png (278.46 KiB) Viewed 368 times
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- mouse_goi_bayes_fitted_iss=1.net
- .net file for mouse representative network
- (15.9 KiB) Downloaded 17 times
- samanthagonzales
- Posts: 41
- Joined: Wed Jun 07, 2023 2:38 pm
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