| Function | Description |
| delta.plot | Delta Plots |
| ebam | Empirical Bayes Analysis of Microarrays |
| ebam.wilc | Empirical Bayes Analysis using Wilcoxon Rank Sums |
| find.a0 | Computation of the Fudge Factor |
| fudge2 | Fudge Factor |
| help.sam | Help files or argument list for SAM-specific methods |
| link.genes | Links for a list of genes |
| link.siggenes | Links for a SAM object |
| list.siggenes | List of the significant genes |
| na.handling | Handling of Missing Values |
| na.replace.cont | Replacing of Missing Values in Continuous Data |
| na.replace.dist | Handling of Missing Values in Categorical Data |
| pi0.est | Estimation of the prior probability |
| qvalue.cal | Computation of the q-value |
| sam | Significance Analysis of Microarray |
| sam2excel | CSV file of a SAM object |
| sam2html | HTML page for a SAM object |
| SAM-class | Class SAM |
| sam.dstat | SAM Analysis Using a Modified t-statistic |
| sam.plot2 | SAM Plot |
| sam.snp | SAM Analysis for Categorical Data |
| sam.wilc | SAM Analysis Using Wilcoxon Rank Statistics |
| sumSAM-class | Class sumSAM |