Microarray Data Analysis

R scripts for analysis of microarray data.
We used microarray data to compare the expression of two different sets of genes from different cells maintained in particular conditions.

Outputs

• Correlation matrix between samples
• Principal component analysis results
• List of the up-regulated genes

The results will save as a PDF document, auto-generated by R Markdown, and store in a folder named output.

Example

We used GEO dataset GSE13601 as an example. In this dataset there are expression data from cigarette smoke-treated mice at 4 and 6 months of age.

• Subjects goups:
control_4: Control mice at 4 months of age
control_6: Control mice at 4 months of age
smoke_4: Cigarette smoke-treated mice at 4 months of age
smoke_6: Cigarette smoke-treated mice at 6 months of age

• Correlation matrix between samples


• Principal component analysis results


• List of the up-regulated genes
upregulated.txt

Requirements
limma, Biobase, GEOquery, pheatmap, ggplot2, plyr, pheatmap