Affymetrix Facility Documentation
 
Affy Facility Docs Home
Running Chips
Pricing
Sample Submission
SBEAMS
Download Data
Annotate Samples
GetExpression
Get Affy Intensity
Analize Data
Analysis Pipeline
MEV
Affy Help Pages
Affy Core Help
SBEAMS Help Pages
Analysis Help Pages
Tutorials and Presentations
Other Resources
Affymetrix Home Page

Affymetrix Analysis Use Cases

These are a series of use cases on how to analyze Affymetrix data


Bioconductor Raw Probe Intensity
See how to Run R/Bioconductor to get Raw Probe Intensities from from Cell files
Open Help Link
R-Raw Probes
RMAExpress
Use a stand-alone windows application to pre-process Affymetrix data with RMA method
Open Help Link
RMAExpress Analysis
Bioconductor RMA Analysis
Use Bioconductor to pre-process Affymetrix data with RMA method
Open Help Link
Bioconductor RMA method
Bioconductor RMA and t-test
Use Bioconductor to pre-process Affymetrix data with RMA method, followed by t-test for differential expression
Open Help Link
Bioconductor RMA/t-test
Make R_CHP files using mas5.0
Reproduce Affymetrix CHP files using R/Bioconductor
Open Help Link
Run R_CHP
R vs. GCOS MAS5
Validate R/bioconductor/affy mas5 against Affymetrix GCOS Software
Open Help Link
R vs GCOS MAS5