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

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<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
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Multiple testing problem. Concepts, Bonferroni correction and FDR)
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<b>Keywords:</b>&nbsp;
 
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Multiple testing problem. Concepts, Bonferroni correction and FDR
 
 
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__TOC__
 
  
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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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 />
 
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<!-- ============================  -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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This unit will ...
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You need to complete the following units before beginning this one:
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* ... introduce the concepts of probability correction with Family Wise Error rate and False Discovery Rate.
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</td>
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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After working through this unit you ...
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* ... are aware of the need to correct significance levels in situations with multiple observations;
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* ... are familar with the ideas of the Bonferroni correction and control with the False Discovery Rate (FDR).
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</td>
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</tr>
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</table>
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<!-- ============================ -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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<li><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.</li>
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<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
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This unit builds on material covered in the following prerequisite units:<br />
 
*[[BIN-EXPR-DE|BIN-EXPR-DE (Discovering Differentially Expressed Genes)]]
 
*[[BIN-EXPR-DE|BIN-EXPR-DE (Discovering Differentially Expressed Genes)]]
 
*[[FND-STA-Significance|FND-STA-Significance (Significance)]]
 
*[[FND-STA-Significance|FND-STA-Significance (Significance)]]
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<section end=prerequisites />
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<!-- ============================  -->
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=== Objectives ===
 
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This unit will ...
 
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* ... introduce the concepts of probability correction with Family Wise Error rate and False Discovery Rate.
 
  
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=== Outcomes ===
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__TOC__
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After working through this unit you ...
 
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* ... are aware of the need to correct significance levels in situations with multiple observations;
 
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* ... are familar with the ideas of the Bonferroni correction and control with the False Discovery Rate (FDR).
 
  
 
{{Vspace}}
 
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=== Deliverables ===
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=== Evaluation ===
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<!-- included from "./components/BIN-EXPR-Multiple_testing.components.txt", section: "deliverables" -->
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<b>Evaluation: NA</b><br />
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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*<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.
 
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<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
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<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
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== Contents ==
 
== Contents ==
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== Further reading, links and resources ==
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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== Notes ==
 
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== Self-evaluation ==
 
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=== Question 1===
 
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<b>If in doubt, ask!</b> 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.
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-11-10
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:2020-09-24
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:1.0
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:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.1 Maintainance
 
*1.0 First live version
 
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 07:08, 25 September 2020

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:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

     

    Task:


     


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-24

    Version:

    1.1

    Version history:

    • 1.1 Maintainance
    • 1.0 First live version
    • 0.1 First stub

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