## Creating a correlation matrix with R

Updated 2014 January 6th This post on creating a correlation matrix with R was published in 2012 on January the 31st and has become one of the most viewed posts. I’ve learned a bit more since then, so I have updated and improved this post. Incentive Let $$A$$ be a $$m \times n$$ matrix, where…

## DESeq vs. edgeR vs. baySeq

6th April 2012: For a more updated version of this post, please refer see this post. A very simple comparison Using the TagSeqExample.tab file from the DESeq package as the benchmark dataset. According to DESeq authors, T1a and T1b are similar, so I removed the second column in the file corresponding to T1a: Hierarchical clustering…

## Hierarchical clustering with p-values

The code, which allowed me to use the Spearman’s rank correlation coefficient, was kindly provided to me by the developer of pvclust. Firstly download the unofficial package or just source it from my DropBox account. Start up R and follow: Hierarchical clustering with p-values.