Yet another statistical microarray analysis

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Documentation for package ‘yasma’ version 0.20

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anova.bfaov ANOVA table of balanced factorial designs
array2rg Balanced factorial array from RG structure
bfaov Efficient ANOVA of balanced factorial designs
coef.bfaov Coefficients and residuals of bfaov ANOVA
data.over.under Analysis of over- and under-expressed genes
diff.vg Significance of variety-gene effects from ANOVA analysis
hist.vg Significance of variety-gene effects from ANOVA analysis
interpolate.bfaov Interpolate missing values in balanced factorial data array
limit.vg Significance of variety-gene effects from ANOVA analysis
log.array2rg Balanced factorial array from RG structure
ma.cor Loess normalization of RG values
ma.plot Plots log G over log R for RG structure
ma.plot.single Plots log G over log R for RG structure
ma.write Interconversion of RG and MA structure
ma2rg Interconversion of RG and MA structure
optim.design REML estimates of variance components
over.under Analysis of over- and under-expression from ANOVA
over.under.level Analysis of over- and under-expression from ANOVA
plot.residuals Coefficients and residuals of bfaov ANOVA
print.reml REML estimates of variance components
pvalue.fdr Benjamini-Hochberg FDR adjustment for multiple testing p-values
read.rg RG structure from microarray data table file
reml.bfaov REML estimates of variance components
reml.kt REML estimates of variance components
residuals.bfaov Coefficients and residuals of bfaov ANOVA
rg.add2bg Background manipulation
rg.cor Correlation between experiments
rg.duplicate.genes Transforms multiple spots into extra experiments
rg.failure.histogram Plot of number of low expression genes
rg.keep Removal of genes and experiments from RG structure
rg.keep.containing Removal of genes and experiments from RG structure
rg.linear.normalize Loess normalization of RG values
rg.loess.array.normalize Loess normalization of RG values over microarray
rg.loess.normalize Loess normalization of RG values
rg.log.matrix Log2 matrix from RG structure
rg.log.plot Plots log G over log R for RG structure
rg.project Removal of genes and experiments from RG structure
rg.rank.normalize Loess normalization of RG values
rg.remove Removal of genes and experiments from RG structure
rg.remove.containing Removal of genes and experiments from RG structure
rg.remove.quantile Removal of genes with low expression levels
rg.rsq Diagnostics of low expression genes
rg.rsq.plot Diagnostics of low expression genes
rg.scale.normalize Loess normalization of RG values
rg.shift.normalize Loess normalization of RG values
rg.sub.bg Background manipulation
rg.write Removal of genes and experiments from RG structure
rg.zero.bg Background manipulation
rg2array Balanced factorial array from RG structure
rg2log.array Balanced factorial array from RG structure
rg2ma Interconversion of RG and MA structure
sd.vg Significance of variety-gene effects from ANOVA analysis
set.formula Efficient ANOVA of balanced factorial designs
stat.Newton.multi Logodds of differential expression derived from hierarchical Gamma models
t.boots t-statistic bootstrap for differential gene expression
t.statistic t-statistic for differential gene expression
t.statistic.2 t-statistic for differential gene expression
write.over.under Analysis of over- and under-expressed genes