Statistical Analysis of the GeneChip


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Documentation for package ‘SAGx’ version 1.40.0

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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
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
plot-method Class "samroc.result" for results of the function samrocN
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)
samroc.result-class Class "samroc.result" for results of the function samrocN
samrocN Calculate ROC curve based SAM statistic
samrocNboot Calculate ROC curve based SAM statistic
show-method 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