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 |

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