Pre-processed Yeast sample RNA-seq data

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Description

Pre-processed Yeast sample RNA-seq data, obtained from the website: http://cgrlucb.wikispaces.com/Spring+2012+DESeq+Tutorial

For more information, please contact the author of the webpage.

The content from the tutorial's webpage is licensed as follows: Contributions to http://cgrlucb.wikispaces.com/ are licensed under a Creative Commons Attribution Share-Alike 3.0 License. Creative Commons Attribution Share-Alike 3.0 License.

Usage

1

Format

An 8 column table defined as such:

  • id — the Gene ID reprented by the row

  • baseMean — mean estimated from both conditions (with normalization by size factors)

  • baseMeanA — mean estimated from the first condition specified as an argument to nbinomTest (in this case, “M”)

  • baseMeanB — mean estimated from the second condition (in this case, “WE”)

  • foldChange — ratio of the estimated means

  • log2FoldChange — log2 of the ratio

  • pval — uncorrected p-value from the negative binomial test

  • padj — p-value adjusted for multiple testing using Benjamini-Hochberg to estimate the false discovery rate

  • resVarA — dispersion estimated from the first condition

  • resVarB — dispersion estimated from the second condition

Source

http://cgrlucb.wikispaces.com/Spring+2012+DESeq+Tutorial

References

Lee, H. “Spring 2012 DESeq Tutorial.” http://cgrlucb.wikispaces.com/Spring+2012+DESeq+Tutorial