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| Describe VeroniqueVoisin/Intranet/Protocol here. | = Protocol = * A to Z protocol to create an EnrichmentMap from gene expression data and using GSEA (Gene Set Enrichment Analysis) |
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| = Protocol = | * How to create a rank file * How to create an expression file * How to run GSEA * How to create a map * What is the next step, how to use the map * How to preprocess the data using R * How to preprocess the data using Excel = FIRST EXAMPLE WITH AFFYMETRIX MICROARRAY DATA = * description of the data == Download the data from GEO == == Installation == * 1) install R (http://www.r-project.org/) * 2) install RStudio (http://www.rstudio.com/) * 3) Go through on online R tutorial (e.g. this one: http://www.cyclismo.org/tutorial/R/) == How to preprocess the data (normalization, QC, differential expression) == == How to update the annotations == == How to create a rank file == == How to create an expression file == == How to run GSEA == == How to create a map == == What is the next step, how to use the map == |
Protocol
A to Z protocol to create an EnrichmentMap from gene expression data and using GSEA (Gene Set Enrichment Analysis)
- How to create a rank file
- How to create an expression file
- How to run GSEA
- How to create a map
- What is the next step, how to use the map
- How to preprocess the data using R
- How to preprocess the data using Excel
FIRST EXAMPLE WITH AFFYMETRIX MICROARRAY DATA
- description of the data
Download the data from GEO
Installation
1) install R (http://www.r-project.org/)
2) install RStudio (http://www.rstudio.com/)
3) Go through on online R tutorial (e.g. this one: http://www.cyclismo.org/tutorial/R/)
How to preprocess the data (normalization, QC, differential expression)
How to update the annotations
How to create a rank file
How to create an expression file
How to run GSEA
How to create a map