Tutorial On Microarray Analysis Using Bioconductor and R (Sample Study)
Tutorial On Microarray Analysis Using Bioconductor and R (Sample Study)
Tools Used
• Bioconductor, http://www.bioconductor.org/, provides open source tools for the
analysis and comprehension of high-throughput genomic data
• R, http://www.r-project.org/, R is a free software environment for statistical computing
and graphics
Data Used
• Resveratrol effect on lung carcinoma cell line - Analysis of lung carcinoma A549 cells
treated with resveratrol. Resveratrol is a phytoestrogen found in red wine. Results
provide insight into protective effect of resveratrol against lung cancer. Available from
the Gene Expression http://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS2966
• 4 CEL files (Micro-array output) Data {GSM228717.CEL, GSM228718.CEL,
GSM228719.CEL, GSM228720.CEL} available from above link
• 1 Sample Phenotype Mapping {GDS296-pheno.csv}
Tasks
1. Import and Normalise data
2. Compare tissue treated with Resveratrol with similar tissue treat with an Ethanol control
3. Filter most differentially expressed genes
4. Cluster and View Analysis
R Code
## Step 1- Load packages
library(affy)
library(limma)
## Step 3 - Import and Normalise Data using functions from the Bioconductor affy
package
eset <- justRMA(phenoData=phenoData)
GDS296-pheno.csv
Sample substance
GSM228717 Control
GSM228718 Wine
GSM228719 Wine
GSM228720 Wine
Notes:
For those interested in more information on Normalisation methods and why RMA (justRMA) is
used, start here:
Bolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003), A Comparison of
Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and
Variance. Bioinformatics 19(2):185-193