SMLG (Statistical Machine Learning Group) Discussion Forum
Changwon Yoo, S.M., Ph.D., PI
GEO datasets
Re: GEO datasets
by lsand039 » Tue Feb 21, 2017 4:24 pm
Here is an initial write up of results from the GMLS obtained from Bene. Attached is the Genie files needed to view the GMLS and the training and test data I used to analyze it.
- Attachments
-
Results-Hippocampus analysis GMLS.docx- Results write up
- (2.38 MiB) Downloaded 149 times
-
- Full data.txt
- Test data
- (27.44 KiB) Downloaded 157 times
-
- Test.txt
- (9.17 KiB) Downloaded 147 times
-
- Hippocampus full data.xdsl
- (23.48 KiB) Downloaded 139 times
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Re: GEO datasets
by lsand039 » Wed Mar 01, 2017 9:28 am
Methods write up with my comments and questions is ready for review.
- Attachments
-
- Methods.docx
- V1
- (49.13 KiB) Downloaded 137 times
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Re: GEO datasets
by lsand039 » Wed Mar 01, 2017 11:09 am
Attached are the initial write ups of the results with comments and questions and the appendices. I wasn't sure how to best organize the graphs where I controlled for Age, Brain Region, Sex, and AD status, so I've included the outline of my results which contain comparisons for Age & Brain Region & Sex; AD & Age & Brain Region; AD & Age & Sex; and AD & Brain Region & Sex.
Also, I checked Bene BDe scores & structure with the Confounding Structure. The Confounding Structure still had a better Log (p) score.
Also, I checked Bene BDe scores & structure with the Confounding Structure. The Confounding Structure still had a better Log (p) score.
- Attachments
-
- Results-Hippocampus analysis.docx
- (4.21 MiB) Downloaded 143 times
-
- Appendix A.docx
- V1
- (5.2 MiB) Downloaded 158 times
-
- Results-Thesis 2.docx
- V1
- (288.68 KiB) Downloaded 156 times
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Re: GEO datasets
by lsand039 » Wed Mar 01, 2017 12:56 pm
Attached is my initial outline for the discussion. You can see updates through this link: https://1drv.ms/w/s!AkaTNPVSS2G6lytUDoa3Qub7exvy
- Attachments
-
- Thesis 2 Discussion Outline.docx
- (15.19 KiB) Downloaded 155 times
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Re: GEO datasets
by lsand039 » Thu Mar 02, 2017 6:21 pm
Bene tests on my data:
(scores are copied directly from the terminal)
I don't understand why I get -nan when I specify BDe scoring or don't specify which scoring to use. I also don't know why I'm getting positive numbers for AIC and BIC scoring, so I wasn't able to find out the percentages of these scores.
AIC
No arcs
Score : 8.000
Score (according to GeNIe): -9255.057410
BDe
Fully connected structure
Score : -nan
Score (according to GeNIe): -8629.672524
BIC
No arcs
Score : 29.081
Score (according to GeNIe): -9255.057410
Not specified
fully connected structure
Score : -nan
Score (according to GeNIe): -8629.672524
(scores are copied directly from the terminal)
I don't understand why I get -nan when I specify BDe scoring or don't specify which scoring to use. I also don't know why I'm getting positive numbers for AIC and BIC scoring, so I wasn't able to find out the percentages of these scores.
AIC
No arcs
Score : 8.000
Score (according to GeNIe): -9255.057410
BDe
Fully connected structure
Score : -nan
Score (according to GeNIe): -8629.672524
BIC
No arcs
Score : 29.081
Score (according to GeNIe): -9255.057410
Not specified
fully connected structure
Score : -nan
Score (according to GeNIe): -8629.672524
- Attachments
-
- Not specified
- IDH.png (121.33 KiB) Viewed 60068 times
-
- BIC result
- IDHbic.png (19.21 KiB) Viewed 60068 times
-
- BDe result
- IDHbde.png (121.33 KiB) Viewed 60068 times
-
- AIC result
- IDHaic.png (19.21 KiB) Viewed 60068 times
Last edited by lsand039 on Tue Mar 07, 2017 11:24 am, edited 1 time in total.
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Re: GEO datasets
by lsand039 » Fri Mar 03, 2017 10:25 am
Attached is my draft of initial discussions with several questions and comments I have.
- Attachments
-
- Discussion Draft.docx
- V1
- (26.94 KiB) Downloaded 146 times
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Re: GEO datasets
by lsand039 » Fri Mar 03, 2017 10:59 pm
Confounding structure:
Log (P): -8617.419198
Log (P): -8617.419198
- Attachments
-
- confounder.dot.png (94.57 KiB) Viewed 60067 times
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Re: GEO datasets
by cwyoo » Sat Mar 04, 2017 3:40 am
lsand039 wrote:Confounding structure:
Log (P): -8617.419198
The log likelihoods are the same for confounding structure and bene BDe structure?
- cwyoo
- Site Admin
- Posts: 387
- Joined: Sun Jun 22, 2014 2:38 pm
Re: GEO datasets
by lsand039 » Mon Mar 06, 2017 1:23 pm
Attached is the genomic data for the datasets that specify race/ ethnicity. They still have to be descritized, but the files attached have the raw expression values connected to the gene name.
- Attachments
-
- GPL84422_570.xlsx
- (10.49 MiB) Downloaded 144 times
-
- GSE5281MAc.xlsx
- (23.59 MiB) Downloaded 155 times
-
- GSE15222MAc.xlsx
- (17.63 MiB) Downloaded 157 times
-
- GSE84422_96MAc.xlsx
- (200.16 MiB) Downloaded 154 times
Last edited by lsand039 on Tue Mar 07, 2017 11:25 am, edited 1 time in total.
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Re: GEO datasets
by lsand039 » Tue Mar 07, 2017 11:23 am
cwyoo wrote:lsand039 wrote:Confounding structure:
Log (P): -8617.419198
The log likelihoods are the same for confounding structure and bene BDe structure?
Oh no! I copied the wrong score! It should be -8629.672524 for the bene BDe structure. I will make corrections to my previous post
- Attachments
-
- Confounding Structure & Score
- Screenshot from 2017-03-07 10-25-31.png (47.61 KiB) Viewed 60066 times
-
- BDe structure & score
- Screenshot from 2017-03-07 10-23-11.png (47.47 KiB) Viewed 60066 times
- lsand039
- Posts: 237
- Joined: Thu Jan 14, 2016 12:17 pm
Who is online
Users browsing this forum: No registered users and 38 guests