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: 2014 April 18th A post showing edgeR's common dispersion values from a set of values generated from various distributions. For an explanation of the common dispersion value in edgeR, please refer to this thread. The generated values represent the counts of reads, i.e., expression level, for a gene. Each row will represent one gene...

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