DrugVsDisease (version 2.12.0)

DrugVsDisease-package: DrugVsDisease Package Overview

Description

This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express [1] or GEO [2], or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma [3]. Enrichment scores [4] are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Significance scores are output in Cytoscape http://www.cytoscape.org/ format.

Details

Package:

DvD

Type:

Package

Version:

1.0

Date:

2012-06-15

License:

GPL-2

LazyLoad:

yes

Profiles are calculated via generateprofiles and selected profiles are then classified using classifyprofile.

References

[1]Parkinson et al. (2010) ArrayExpress update an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucl. Acids Res.,doi: 10.1093/nar/gkq1040.

[2]Barrett T et al. (2011) NCBI GEO: archive for functional genomics data sets-10 years on. Nucl. Acids Res, 39, D1005-D1010.

[3]Smyth et al. (2004). Linear models and empirical Bayes method for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3.

[4]Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.

See Also

generateprofiles, selectrankedlists, classifyprofile

Examples

profiles<-generateprofiles(input="GEO",accession="GDS2617",case="disease",statistic="t",annotation="hgu133a")
selprofile<-selectrankedlists(profiles,6)
classification<-classifyprofile(data=selprofile$ranklist,signif.fdr=1,noperm=20)