edgeR vs. DESeq using pnas_expression.txt

Firstly from Davis's homepage download the file pnas_expression.txt. For more information on the dataset please refer to the edgeR manual and this paper. The latest R version at the time of writing is R 2.13.1. You can download it from here. Install bioconductor and the required packages: source(“http://www.bioconductor.org/biocLite.R”) biocLite() biocLite(“DESeq”) biocLite(“edgeR”) A filtering criteria of...

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Pearson vs. Spearman correlation

Correlation measures are commonly used to show how correlated two sets of datasets are. A commonly used measure is the Pearson correlation. To illustrate when not to use a Pearson correlation: If we remove the 2,000 value: Use a non-parametric correlation (e.g. Spearman's rank) measure if your dataset has outliers. It would probably be best...

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edgeR's common dispersion

Updated: 2017 September 7th When I was first learning about conducting a differential expression (DE) analysis with RNA-seq data, I found it very difficult to understand the statistical procedures implemented in various R packages that performed the DE analysis. This really bugged me. However, it was not difficult to carry out the analysis, since the...

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