Difference between revisions of "RPR-GEO2R"

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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%;">
 
GEO2R
 
GEO2R
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  </div>
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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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(Programming for analysis of GEO datasets)
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  {{Vspace}}
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Programming for analysis of GEO datasets
 
 
</div>
 
</div>
  
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{{Smallvspace}}
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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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{{LIVE}}
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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</div>
 
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "../components/RPR-GEO2R.components.wtxt", section: "abstract" -->
 
 
This unit demonstrates accessing and working with datasets downloaded from NCBI GEO.
 
This unit demonstrates accessing and working with datasets downloaded from NCBI GEO.
 
<section end=abstract />
 
<section end=abstract />
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</div>
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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/RPR-GEO2R.components.wtxt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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<!-- included from "ABC-unit_components.wtxt", section: "notes-external_prerequisites" -->
 
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You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:
 
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<!-- included from "FND-prerequisites.wtxt", section: "central_dogma" -->
 
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*<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
 
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You need to complete the following units before beginning this one:
 
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*[[BIN-EXPR-Multiple_testing|BIN-EXPR-Multiple_testing (Multiple Testing and Significance)]]
 
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{{Vspace}}
 
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−
 
 
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=== Objectives ===
 
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<!-- included from "../components/RPR-GEO2R.components.wtxt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* ... teach downloading and annotating GEO data, and performing differential expression analysis.
 
* ... teach downloading and annotating GEO data, and performing differential expression analysis.
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</td>
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{{Vspace}}
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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=== Outcomes ===
 
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<!-- included from "../components/RPR-GEO2R.components.wtxt", section: "outcomes" -->
 
 
After working through this unit you ...
 
After working through this unit you ...
 
* ... can access GEO data;
 
* ... can access GEO data;
 
* ... are familar with the structure of GEO expression sets;
 
* ... are familar with the structure of GEO expression sets;
 
* ... can annotate the data, perform differential expression anlysis and critically evaluate the results.
 
* ... can annotate the data, perform differential expression anlysis and critically evaluate the results.
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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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<!-- ============================  -->
 +
<hr>
 +
<section begin=prerequisites />
 +
<b>Prerequisites:</b><br />
 +
You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:<br />
 +
*<b>The Central Dogma</b>: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.
 +
This unit builds on material covered in the following prerequisite units:<br />
 +
*[[BIN-EXPR-Multiple_testing|BIN-EXPR-Multiple_testing (Multiple Testing and Significance)]]
 +
<section end=prerequisites />
 +
<!-- ============================  -->
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</div>
  
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{{Vspace}}
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{{Smallvspace}}
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{{Smallvspace}}
  
  
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=== Deliverables ===
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__TOC__
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<!-- included from "../components/RPR-GEO2R.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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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.
 
−
<!-- included from "ABC-unit_components.wtxt", 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 "ABC-unit_components.wtxt", 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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=== Evaluation ===
 
=== Evaluation ===
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<!-- included from "../components/RPR-GEO2R.components.wtxt", section: "evaluation" -->
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This learning unit can be evaluated for a maximum of 5 marks. If you choose to submit tasks from this unit for credit:
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This learning unit can be evaluated for a maximum of 6 marks. If you want to submit the tasks for this unit for credit:
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<ol>
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# Create a new page on the student Wiki as a subpage of your User Page.
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<li>Create a new page on the student Wiki as a subpage of your User Page.</li>
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# There are a number of tasks in which you are explicitly asked you to submit code or other text for credit. Put all of these submission on this one page.
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<li>The R-script for this unit contains a number of tasks in which you are explicitly asked to submit code or results for credit. Put all of your writing to submit on this one page.</li>
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# When you are done with everything, add the following category tag to the page:
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<li>When you are done with everything, go to the [https://q.utoronto.ca/courses/180416/assignments Quercus '''Assignments''' page] and open the first Learning Unit that you have not submitted yet. Paste the URL of your Wiki page into the form, and click on '''Submit Assignment'''.</li>
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::<code><nowiki>[[Category:EVAL-RPR-GEO2R]]</nowiki></code>
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</ol>
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'''Do not''' change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.
 
  
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Your link can be submitted only once and not edited. But you may change your Wiki page at any time. However only the last version before the due date will be marked. All later edits will be silently ignored.
  
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</div>
 
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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<!-- included from "../components/RPR-GEO2R.components.wtxt", section: "contents" -->
 
  
 
{{ABC-unit|RPR-GEO2R.R}}
 
{{ABC-unit|RPR-GEO2R.R}}
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== Further reading, links and resources ==
 
== Further reading, links and resources ==
 
<!-- {{#pmid: 19957275}} -->
 
<!-- {{#pmid: 19957275}} -->
 
<div class="reference-box">This unit has focussed on microarray analysis with GEO2R. For RNAseq experiments, refer to the excellent [https://www.bioconductor.org/help/workflows/RNAseq123/ '''Bioconductor RNAseq analysis tutorial'''].</div>
 
<div class="reference-box">This unit has focussed on microarray analysis with GEO2R. For RNAseq experiments, refer to the excellent [https://www.bioconductor.org/help/workflows/RNAseq123/ '''Bioconductor RNAseq analysis tutorial'''].</div>
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== Notes ==
 
== Notes ==
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== Self-evaluation ==
 
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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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<div class="about">
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-11-11
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:2020-10-07
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:1.0
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:1.2
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.2 Edit policy update
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*1.1 2020 Updates; all online
 
*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 05:02, 10 October 2020

GEO2R

(Programming for analysis of GEO datasets)


 


Abstract:

This unit demonstrates accessing and working with datasets downloaded from NCBI GEO.

Objectives:
This unit will ...

  • ... teach downloading and annotating GEO data, and performing differential expression analysis.

Outcomes:
After working through this unit you ...

  • ... can access GEO data;
  • ... are familar with the structure of GEO expression sets;
  • ... can annotate the data, perform differential expression anlysis and critically evaluate the results.

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:
    You need the following preparation before beginning this unit. If you are not familiar with this material from courses you took previously, you need to prepare yourself from other information sources:

    • The Central Dogma: Regulation of transcription and translation; protein biosynthesis and degradation; quality control.

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


     



     



     


    Evaluation

    This learning unit can be evaluated for a maximum of 5 marks. If you choose to submit tasks from this unit for credit:

    1. Create a new page on the student Wiki as a subpage of your User Page.
    2. The R-script for this unit contains a number of tasks in which you are explicitly asked to submit code or results for credit. Put all of your writing to submit on this one page.
    3. When you are done with everything, go to the Quercus Assignments page and open the first Learning Unit that you have not submitted yet. Paste the URL of your Wiki page into the form, and click on Submit Assignment.

    Your link can be submitted only once and not edited. But you may change your Wiki page at any time. However only the last version before the due date will be marked. All later edits will be silently ignored.


     

    Contents

    Task:

     
    • Open RStudio and load the ABC-units R project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
    • Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
    • Type init() if requested.
    • Open the file RPR-GEO2R.R and follow the instructions.


     

    Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.


     

    Further reading, links and resources

    This unit has focussed on microarray analysis with GEO2R. For RNAseq experiments, refer to the excellent Bioconductor RNAseq analysis tutorial.

    Notes


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-10-07

    Version:

    1.2

    Version history:

    • 1.2 Edit policy update
    • 1.1 2020 Updates; all online
    • 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=RPR-GEO2R&oldid=11847"