https://github.com/jorainer/rnw-based-affy-analysis
Standard analysis of Affymetrix microarrays defined using Rnw files.
https://github.com/jorainer/rnw-based-affy-analysis
Last synced: 3 months ago
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Standard analysis of Affymetrix microarrays defined using Rnw files.
- Host: GitHub
- URL: https://github.com/jorainer/rnw-based-affy-analysis
- Owner: jorainer
- Created: 2014-10-28T09:15:15.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2014-10-28T09:20:29.000Z (over 10 years ago)
- Last Synced: 2025-01-20T22:55:03.469Z (5 months ago)
- Language: TeX
- Size: 816 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README
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README
* Requirements: a recent R with Bioconductor installed. Additional packages can be
installed with the shell script in source/shell/install_packages.sh. Note that for
Gene ST microarrays it is also required to install the appropriate CDF and probe
packages (from http://bioinfo.i-med.ac.at).
* Rename folder and "MAIN-affymetrix-analysis.tex" according to the project.
* Define a phenodata file (e.g. phenodata.txt) and put it in data/txt. This file should
list all microarrays of the experiment and define the groups. Required/suggested columns
are: CEL, name, group.
* Modify the rawdata-preprocessing.Rnw according to the setup. Note: this file works only
for the "older" 3' microarrays (e.g. hgu133plus2). To analyze newer generation microarrays
(i.e. gene ST microarrays), use the rawdata-preprocessing-gene-st.Rnw. In the latter case
CDF and probe packages have to be installed for the microarray from http://bioinfo.i-med.ac.at.
* Differential expression analysis is defined in diffexp.Rnw.
* The Rnw and the basic set up of this type of analysis was defined and set-up by:
- Julien Lelong
- Daniel Bindreither
- Johannes Rainer