# SAM: Significance Analysis of Microarrays

## Documentation for package ‘samr’ version 3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

runSAM | Run the sam webapp
SAM | Significance analysis of microarrays - simple user interface
samr | Significance analysis of microarrays
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.compute.delta.table | Compute delta table for SAM analysis
samr.compute.siggenes.table | Compute significant genes table
samr.estimate.depth | estimate the sequencing depth
samr.missrate | Estimate the miss rate table for a SAM analysis
samr.norm.data | output normalized sequencing data
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.tail.strength | Estimate tail strength for a dataset, from a SAM analysis
SAMseq | Significance analysis of sequencing data - simple user interface