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| args.ebam | Help files or argument list for EBAM-specific methods |
| args.finda0 | Help files or argument list for FindA0-specific methods |
| args.sam | Help files or argument list for SAM-specific methods |
| cat.ebam | EBAM Analysis for Categorical Data |
| cat.stat | SAM Analysis for Categorical Data |
| chisq.ebam | EBAM Analysis for Categorical Data |
| chisq.stat | SAM Analysis for Categorical Data |
| d.stat | SAM Analysis Using a Modified t-statistic |
| delta.plot | Delta Plots |
| denspr | Density Estimation |
| EBAM | Class EBAM |
| ebam | Empirical Bayes Analysis of Microarrays |
| EBAM-class | Class EBAM |
| ebam2excel | CSV file of a SAM or an EBAM object |
| ebam2html | HTML page for a SAM or an EBAM object |
| ebamControl | Further EBAM Arguments |
| find.a0 | Computation of the Fudge Factor |
| find.a0Control | Further EBAM Arguments |
| FindA0 | Class FindA0 |
| FindA0-class | Class FindA0 |
| findDelta | Finding the Threshold Delta |
| fudge2 | Fudge Factor |
| fuzzy.ebam | EBAM and SAM for Fuzzy Genotype Calls |
| fuzzy.stat | EBAM and SAM for Fuzzy Genotype Calls |
| help.ebam | Help files or argument list for EBAM-specific methods |
| help.finda0 | Help files or argument list for FindA0-specific methods |
| help.sam | Help files or argument list for SAM-specific methods |
| identify-method | Class SAM |
| limma2ebam | limma to SAM or EBAM |
| limma2sam | limma to SAM or EBAM |
| link.genes | Links for a list of genes |
| link.siggenes | Links for a SAM or an EBAM object |
| list.siggenes | List of the significant genes |
| md.plot | MD Plot |
| nclass.wand | Number of cells in a histogram |
| pi0.est | Estimation of the prior probability |
| plot-method | Class EBAM |
| plot-method | Class FindA0 |
| plot-method | Class SAM |
| plotArguments | Plot Arguments |
| plotFindArguments | Plot Arguments |
| print-method | Class EBAM |
| print-method | Class FindA0 |
| print-method | Class SAM |
| print-method | Classes sumSAM and sumEBAM |
| qvalue.cal | Computation of the q-value |
| rowRanksWilc | Rowwise Wilcoxon Rank Sum Statistics |
| rowWilcoxon | Rowwise Wilcoxon Rank Sum Statistics |
| SAM | Class SAM |
| sam | Significance Analysis of Microarray |
| SAM-class | Class SAM |
| sam.plot2 | SAM Plot |
| sam2excel | CSV file of a SAM or an EBAM object |
| sam2html | HTML page for a SAM or an EBAM object |
| samControl | Further SAM Arguments |
| show-method | Class EBAM |
| show-method | Class FindA0 |
| show-method | Class SAM |
| show-method | Classes sumSAM and sumEBAM |
| siggenes2excel | CSV file of a SAM or an EBAM object |
| siggenes2html | HTML page for a SAM or an EBAM object |
| sumEBAM-class | Classes sumSAM and sumEBAM |
| summary-method | Class EBAM |
| summary-method | Class SAM |
| sumSAM-class | Classes sumSAM and sumEBAM |
| trend.ebam | EBAM Analysis of Linear Trend |
| trend.ebam.data.frame | EBAM Analysis of Linear Trend |
| trend.ebam.default | EBAM Analysis of Linear Trend |
| trend.ebam.list | EBAM Analysis of Linear Trend |
| trend.stat | SAM Analysis of Linear Trend |
| trend.stat.data.frame | SAM Analysis of Linear Trend |
| trend.stat.default | SAM Analysis of Linear Trend |
| trend.stat.list | SAM Analysis of Linear Trend |
| wilc.ebam | EBAM Analysis Using Wilcoxon Rank Statistics |
| wilc.stat | SAM Analysis Using Wilcoxon Rank Statistics |
| z.ebam | EBAM analysis Using t- or F-test |
| z.find | EBAM analysis Using t- or F-test |