Statistical Analysis of the GeneChip


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Documentation for package `SAGx' version 1.5.2

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caha Clustering Goodness measured by the Calinski-Harabasz index
clin2mim Output a script file to WinMIM, linking clinical data and gene expression
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
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
nn.impute Impute mean based on k nearest neighbours
normalise Normalise arrays
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
permutation.t bootstrap p-value for matrix with variables in rows and with arbitrary missing structure.
R2mim Output a script file to WinMIM
rank.genes Rank genes with respect to multiple criteria
rank.trend Trens 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
Xprep Calculation of input to stat.bayesian starting from linear model
Zfreq Bayesian analysis of a Comparative experiment with two groups