Cancer Bioinformatics Workshop, Cambridge 2010

The Importance of Reproducible Research in High-Throughput Biology: Case Studies in Forensic Bioinformatics

author: Keith A. Baggerly, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston
published: Oct. 11, 2010, recorded: September 2010, views: 4524

Slides

Slides
0:00	The Importance of Reproducibility in High-Throughput Biology: Case Studies in Forensic Bioinformatics
1:19	Why is RR So Important in H-TB?
2:43	Using the NCI60 to Predict Sensitivity
5:19	Fit Training Data
5:58	Fit Testing Data
6:46	5-FU Heatmaps - 1
7:21	5-FU Heatmaps - 2
7:30	5-FU Heatmaps - 3
7:46	Their List and Ours
8:28	Offset P-Values: Other Drugs
9:02	Using Their Software
10:00	Heatmaps Match Exactly for Most Drugs! - 1
10:45	Heatmaps Match Exactly for Most Drugs! - 2
11:34	Predicting Docetaxel (Chang 03)
12:36	Predicting Adriamycin (Holleman 04)
13:51	There Were Other Genes...
15:12	RR Theme: Don’t Take My Word For It!
15:45	Potti/Nevins Reply (Nat Med 13:1277-8)
16:51	Adriamycin 0.9999 + Correlations (Reply) - 1
17:54	Adriamycin 0.9999 + Correlations (Reply) - 2
18:22	The First 20 Files Now Named
19:14	Validation 1: Hsu et al
20:29	The 4 We Can’t Match (Reply)
21:00	Some Timeline Here... - 1
21:12	Some Timeline Here... - 2
21:44	Some Timeline Here... - 3
22:00	Jan 29, 2010
22:21	Why We’re Unhappy... - 1
22:44	Why We’re Unhappy... - 2
23:25	We Tried Matching The Samples
24:36	FOI(L)A! - 1
24:54	FOI(L)A! - 2
25:32	May 14, 2010
25:53	July 16, 2010
26:21	July 19, 2010
26:48	Subsequent Events, and a Caveat - 1
27:13	Subsequent Events, and a Caveat - 2
27:30	Some Observations
28:09	What Should the Norm Be?
28:38	Some Lessons
29:42	- Questions

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