The R package for SAFE (version 2.0) is available on Bioconductor
Go to Bioconductor
and follow the links to Release Packages for this version of SAFE.
SAFE version 2.0 incorporates features from Barry et al. 2008 including several functions to
enhance the presentation and plotting of results.
A vignette for SAFE is available with the Bioconductor package; provided here are archived
source code, example of usage,
and vignette
created during the development of SAFE v2.0.
Additional functions and source code for the EORTC-NCI-ASCO 2011 Annual Meeting
are available by request from Bill Barry. All questions and comments regarding SAFE are appreciated
|
Barry WT, Nobel AB, Wright FA. (2005)
Significance analysis of functional categories in gene expression studies:
a structured permutation approach.
Bioinformatics 21(9):1943-9.
Supplementary Table Supplementary Figure 1 Supplementary Figure 2 Supplementary Figure 3 Supplementary Figure 4 Barry WT, Nobel AB, Wright FA. (2008) "A statistical framework for testing functional categories in microarray data ." Annals of Applied Statistics 2(1):286-315. Gatti DM, Sypa M, Rusyn I, Wright FA, Barry WT (2009) " SAFEGUI: Resampling-Based Tests of Categorical Significance in Gene Expression Data Made Easy." Bioinformatics 25(4): 541-2, Gatti DM, Barry WT, Nobel AB, Rusyn I, Wright FA (2010) "Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets." BMC Genomics. 11:574 EORTC-NCI-ASCO Annual Meeting 2011 "A genomic-based signature of response to chemotherapy in ovarian cancer fails to predict clinical outcome in two independent cohorts" William Barry Slides |