Expected Preparations:

  The Central Dogma:
Regulation of transcription and translation; Protein biosynthesis and degradation; Quality control.
   [BIN-EXPR]
Multiple_testing 		 
  If you are not already familiar with the prior knowledge listed above, you need to prepare yourself from other information sources.   The units listed above are part of this course and contain important preparatory material.  
Keywords: Programming for analysis of GEO datasets
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.

Evaluation:

Evaluation deliverables under revision:
While we are rebalancing formative feedback (advice) and summative feedback (grades) for this course, please ignore all instructions for the submission of assignments until this alert is removed.

 

Contents

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

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. This ensures that your data and code remain up to date when we update, or fix bugs.
  • 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

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

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: RPR-GEO2R

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
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
Tagged with:
–  Unit
–  Live
–  Evaluated unit
–  Links to R course project
–  Has further reading

 

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