PT  - JOURNAL ARTICLE
AU  - Andrew Anand Brown
TI  - LargeQvalue: A Program for Calculating FDR Estimates with Large Datasets
AID  - 10.1101/010074
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 010074
4099  - http://biorxiv.org/content/early/2015/03/18/010074.short
4100  - http://biorxiv.org/content/early/2015/03/18/010074.full
AB  - This is an implementation of the R statistical software qvalue package [Dabney et al., 2014], designed for use with large datasets where memory or computation time is limiting. In addition to estimating p values adjusted for multiple testing, the software outputs a script which can be pasted into R to produce diagnostic plots and report parameter estimates. This program runs almost 30 times faster and requests substantially less memory than the qvalue package when analysing 10 million p values on a high performance cluster. The software has been used to control for the multiple testing of 390 million tests when analysing a full cis scan of RNA-seq exon level gene expression from the Eurobats project [Brown et al., 2014]. The source code and links to executable files for linux and Mac OSX can be found here: https://github.com/abrown25/qvalue. Help for the package can be found by running ./largeQvalue --help.