Difference between revisions of "BIN-EXPR-Multiple testing"

From "A B C"
Jump to navigation Jump to search
m
m
Line 1: Line 1:
−
<div id="BIO">
+
<div id="ABC">
−
  <div class="b1">
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Multiple Testing and Significance
 
Multiple Testing and Significance
−
  </div>
+
<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
−
 
+
(Multiple testing problem. Concepts, Bonferroni correction and FDR)
−
  {{Vspace}}
+
</div>
−
 
 
−
<div class="keywords">
 
−
<b>Keywords:</b>&nbsp;
 
−
Multiple testing problem. Concepts, Bonferroni correction and FDR
 
 
</div>
 
</div>
  
−
{{Vspace}}
+
{{Smallvspace}}
  
  
−
__TOC__
+
<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
−
 
+
<div style="font-size:118%;">
−
{{Vspace}}
+
<b>Abstract:</b><br />
−
 
 
−
 
 
−
{{LIVE}}
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
</div>
 
−
<div id="ABC-unit-framework">
 
−
== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
−
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "abstract" -->
 
 
Searching for significant effects in high-throughput experiments changes the statistical odds of finding highly unusual outcomes. This needs to be properly corrected, especially in situations like expression analysis where we observe tens of thousands of measurements simultaneously and need to determine which ones should be followed up on.
 
Searching for significant effects in high-throughput experiments changes the statistical odds of finding highly unusual outcomes. This needs to be properly corrected, especially in situations like expression analysis where we observe tens of thousands of measurements simultaneously and need to determine which ones should be followed up on.
 
<section end=abstract />
 
<section end=abstract />
−
 
+
</div>
−
{{Vspace}}
+
<!-- ============================ -->
−
 
+
<hr>
−
 
+
<table>
−
== This unit ... ==
+
<tr>
−
=== Prerequisites ===
+
<td style="padding:10px;">
−
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "prerequisites" -->
+
<b>Objectives:</b><br />
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 
−
You need to complete the following units before beginning this one:
 
−
*[[BIN-EXPR-DE|BIN-EXPR-DE (Discovering Differentially Expressed Genes)]]
 
−
*[[FND-STA-Significance|FND-STA-Significance (Significance)]]
 
−
 
 
−
{{Vspace}}
 
−
 
 
−
 
 
−
=== Objectives ===
 
−
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* ... introduce the concepts of probability correction with Family Wise Error rate and False Discovery Rate.
 
* ... introduce the concepts of probability correction with Family Wise Error rate and False Discovery Rate.
−
 
+
</td>
−
{{Vspace}}
+
<td style="padding:10px;">
−
 
+
<b>Outcomes:</b><br />
−
 
 
−
=== Outcomes ===
 
−
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "outcomes" -->
 
 
After working through this unit you ...
 
After working through this unit you ...
 
* ... are aware of the need to correct significance levels in situations with multiple observations;
 
* ... are aware of the need to correct significance levels in situations with multiple observations;
 
* ... are familar with the ideas of the Bonferroni correction and control with the False Discovery Rate (FDR).
 
* ... are familar with the ideas of the Bonferroni correction and control with the False Discovery Rate (FDR).
−
 
+
</td>
−
{{Vspace}}
+
</tr>
−
 
+
</table>
−
 
+
<!-- ============================ -->
−
=== Deliverables ===
+
<hr>
−
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "deliverables" -->
+
<b>Deliverables:</b><br />
 +
<section begin=deliverables />
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
 
*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
Line 71: Line 44:
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 +
<section end=deliverables />
 +
<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
 +
This unit builds on material covered in the following prerequisite units:
 +
*[[BIN-EXPR-DE|BIN-EXPR-DE (Discovering Differentially Expressed Genes)]]
 +
*[[FND-STA-Significance|FND-STA-Significance (Significance)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
 +
</div>
 +
 +
{{Smallvspace}}
 +
 +
 +
 +
{{Smallvspace}}
 +
 +
 +
__TOC__
  
 
{{Vspace}}
 
{{Vspace}}
  
  
−
</div>
 
−
<div id="BIO">
 
 
== Contents ==
 
== Contents ==
 
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "contents" -->
 
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "contents" -->
Line 85: Line 77:
  
 
{{Vspace}}
 
{{Vspace}}
−
 
−
{{Vspace}}
 
−
 
−
 
−
== Further reading, links and resources ==
 
−
<!-- {{#pmid: 19957275}} -->
 
−
<!-- {{WWW|WWW_GMOD}} -->
 
−
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
−
 
−
{{Vspace}}
 
−
 
−
 
−
== Notes ==
 
−
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "notes" -->
 
−
<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
 
−
<references />
 
−
 
−
{{Vspace}}
 
−
 
−
 
−
</div>
 
−
<div id="ABC-unit-framework">
 
 
== Self-evaluation ==
 
== Self-evaluation ==
−
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "self-evaluation" -->
 
 
<!--
 
<!--
 
=== Question 1===
 
=== Question 1===
Line 125: Line 94:
  
 
-->
 
-->
−
 
+
== Notes ==
−
{{Vspace}}
+
<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "notes" -->
−
 
+
<!-- included from "./data/ABC-unit_components.txt", section: "notes" -->
−
 
+
<references />
 +
== Further reading, links and resources ==
 +
<!-- {{#pmid: 19957275}} -->
 +
<!-- {{WWW|WWW_GMOD}} -->
 +
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
  
 
{{Vspace}}
 
{{Vspace}}

Revision as of 19:31, 26 January 2018

Multiple Testing and Significance

(Multiple testing problem. Concepts, Bonferroni correction and FDR)


 


Abstract:

Searching for significant effects in high-throughput experiments changes the statistical odds of finding highly unusual outcomes. This needs to be properly corrected, especially in situations like expression analysis where we observe tens of thousands of measurements simultaneously and need to determine which ones should be followed up on.

Objectives:
This unit will ...

  • ... introduce the concepts of probability correction with Family Wise Error rate and False Discovery Rate.

Outcomes:
After working through this unit you ...

  • ... are aware of the need to correct significance levels in situations with multiple observations;
  • ... are familar with the ideas of the Bonferroni correction and control with the False Discovery Rate (FDR).

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

Prerequisites:
This unit builds on material covered in the following prerequisite units:


 



 



 


Contents

 

Task:


 

Self-evaluation

Notes

Further reading, links and resources

 



 

If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.


 

About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-11-10

Version:

1.0

Version history:

  • 1.0 First live version
  • 0.1 First stub

CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-EXPR-Multiple_testing&oldid=10795"