Monthly Archives: July 2011

edgeR vs. DESeq using pnas_expression.txt

Posted on July 27, 2011 by Davo

Firstly from Davis’s homepage download the file pnas_expression.txt. For more information on the dataset please refer to the edgeR manual. The latest R version at the time of writing is R 2.13.1. You can download it from here. Install bioconductor … Continue reading →

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Pearson vs. Spearman correlation

Posted on July 27, 2011 by Davo

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 … Continue reading →

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edgeR’s common dispersion

Posted on July 27, 2011 by Davo

Please refer to this thread for an explanation of the common dispersion value in edgeR. Script to prepare R script I made a file with 1,000 elements with 4 replicates with exactly the same counts per element: id one two … Continue reading →

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