Man pages for SAGx
Statistical Analysis of the GeneChip
| clin2mim | Output a script file to WinMIM, linking clinical data and... |
| cluster.q | Clustering Goodness measured by Q2 |
| estimatep0 | Estimate proportion unchanged genes |
| fetchSignal | Fetch data from the GATC database |
| firstpass | First pass description of GeneChip data |
| fom | Clustering Figure of Merit |
| fp.fn | Calculation of fp and fn based on a vector of p-values |
| Fstat | Calculation of F statistic by gene given a linear model |
| gap | GAP statistic clustering figure of merit |
| GSEA.mean.t | Gene Set Enrichment Analysis using output from samroc |
| JT.test | Jonckheere-Terpstra trend test |
| list.experiments | Display all experiment names and id's |
| list.intersection.p | p-value for intersection of two gene lists. |
| mat2TeX | Ouput matrix to LaTeX |
| myclus | A clustering function |
| normalise | Normalise arrays |
| one.probeset.per.gene | Select the best probeset per gene |
| outlier | Identify outliers in the multivariate distribution |
| p0.mom | Estimate proportion unchanged genes |
| pava | Pooling of Adjacent Violators |
| pava.fdr | Estimate of the FDR and the proportion unchanged genes |
| R2BASE | Produces a BASE file |
| R2mim | Output a script file to WinMIM |
| rank.genes | Rank genes with respect to multiple criteria |
| rank.trend | Trend analysis based on ranks |
| rsd.test | Compare two groups with respect to their RSD (CV) |
| samrocn | Calculate ROC curve based SAM statistic |
| samrocnboot | Calculate ROC curve based SAM statistic |
| samroc.result-class | Class "samroc.result" for results of the function samrocN |
| union.of.pways | Create the union of two pathway lists |
| Xprep | Fitting of a linear model |
| Xprep.resid | Calculation of input of residuals from linear model |
