Creating a correlation matrix with R

Updated 2024 April 7th Incentive Let be a matrix, where are elements of , where is the row and is the column. If the matrix contained transcript expression data, then is the expression level of the transcript in the assay. The elements of the row of form the transcriptional response of the transcript. The elements…

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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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