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…

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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…

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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.

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