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,samroc.result-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 |
Trens 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,samroc.result-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 |