Editing
Ns126:Calendar/NOTES/2015-12-30
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
===5, Diagnosis biomarker identification and prediction accuracy=== In our RRBS dataset, we have 30 colon cancer plasma, 29 lung cancer plasma, 10 pancreatic cancer plasma and 20 normal plasma. Cancer specific MHL biomarkers were then identified by differential analysis with multiple test correction (Bonferroni corrected P-value <0.5 <span style="color:red">(WHY USE A CUTOFF OF 0.5?? CAN YOU DO FDR?</span>). We identified 1743, 1442 and 614 significant different MHL regions between colon, lung as well as pancreatic cancer and normal, respectively. With the most significant difference 15 MHL regions, the diagnostic sensitivity for colon cancer, lung cancer and pancreatic cancer could come up to 90%, 93.2% and 95%, respectively (See supplementary Tables).<span style="color:red">(HOW DO THE SENSITIVITY CHANGE AS YOU CHANGE THE NUMBER OF MARKERS?)</span> <span style="color:blue">Response: CUTOFF OF 0.5 is not raw P-value, it's P-value after Bonferroni corrected. Bonferroni corrected is more strict than FDR correct. of course, we can choose FDR. if we use FDR correct, more differential region would come out. Here it is very tricky, of course, if we increase the number of the marker, more less power biomarker would come into the prediction model, therefore, the prediction accuracy would be decreased. Here, I want to show the prediction performance in single cancer is more accurate, therefore, I only selected several powerful bio-marker. if we increase this number to hundred or thousand, the prediction accuracy would be decrease to 0.7-0.8, or even lower.</span> <span style="color:blue">Response: Do it again. Change one stage to two stage and take normal tissues as the control in batch 1 and batch 2</span>
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information