am.trans |
Transform replicated arrays into (A,M) format |
baseOlig.error |
Evaluates LPE variance function of M for quantiles of A within and
experimental condition and then interpolates it for all genes. |
baseOlig.error.step1 |
Evaluates LPE variance function of M for quantiles of A within and experimental condition by divinding the A in 100 intervals. |
baseOlig.error.step2 |
Evaluates LPE variance function of M for quantiles of A within and
experimental condition. It is based on the adaptive number of intervals. |
fdr.adjust |
FDR adjustment procedures |
fixbounds.predict.smooth.spline |
Makes the predicted variance non negative |
iqr |
Inter-quartile range |
Ley |
Gene Expression Data from Mouse Immune response study, (2002) |
lowess.normalize |
lowess normalization of the data (based on M vs A graph) |
lpe |
Evaluates local pooled error significance test |
mt.rawp2adjp.LPE |
Adjusted p-values for simple multiple testing procedures |
n.genes.adaptive.int |
Calcuates the number of genes in various intervals adaptively. |
permute |
Calculating all possible permutations of a vector |
preprocess |
Preprocessing the data (IQR normalization, thresholding, log-
transformation, and lowess normalization) |
quan.norm |
Finding quartile range |
quartile.normalize |
Normalization based on quartile range |
resamp.adj |
Resampling based fdr adjustment |