samr v3.0

0

0th

Percentile

SAM: Significance Analysis of Microarrays

Significance Analysis of Microarrays for differential expression analysis, RNAseq data and related problems.

Web-enabled and Cross-platform SAM via Shiny

This version of SAM provided adds a web interface using Shiny.

Install the current version of the package, after removing any older versions you may have already installed. Later, when this package makes it to CRAN, you will install it the usual way.

The web interface is invoked via:

library(samr)
runSAM()


That will bring up a browser window with a user interface. More details are provided in the manual sam.pdf in this directory

Note that users should use Firefox or Chrome as the _default_browser on Windows: IE will not work.

Michael Seo

Functions in samr

 Name Description runSAM Run the sam webapp SAM Significance analysis of microarrays - simple user interface SAMseq Significance analysis of sequencing data - simple user interface samr.plot Make Q-Q plot for SAM analysis samr.pvalues.from.perms Report estimated p-values for each gene, from a SAM analysis samr.estimate.depth estimate the sequencing depth samr-internal Internal samr functions samr.missrate Estimate the miss rate table for a SAM analysis samr.norm.data output normalized sequencing data samr.compute.delta.table Compute delta table for SAM analysis samr.compute.siggenes.table Compute significant genes table samr.tail.strength Estimate tail strength for a dataset, from a SAM analysis samr.assess.samplesize Assess the sample size for a SAM analysis samr.assess.samplesize.plot Make a plot of the results from samr.assess.samplesize samr Significance analysis of microarrays No Results!