alpha.approxeb | Estimate the prior weight, alpha |
approx.expected.info | Approximate of expected information (Fisher information) |
condLogLikDerDelta | Conditional log-likelihood in terms of delta |
condLogLikDerSize | Conditional log-likelihood in terms of size |
deDGE | Compute moderated differential expression scores for digital gene expression (DGE) data |
deDGEList-class | differential expression of Digital Gene Expression data - class |
DGEList | Digital Gene Expression data - class |
DGEList-class | Digital Gene Expression data - class |
EBList-class | differential expression of Digital Gene Expression data - class |
estimatePs | Estimate expression proportions |
exactTestNB | An exact test for differences between two negative binomial groups |
findMaxD2 | Maximizes the negative binomial likelihood |
getData | Extract data table from DGEList object |
interpolateHelper | Quantile Adjustment interpolator |
logLikDerP | Log-likelihood for proportion |
plotMA | MA-like plot for deDGEList objects |
plotMA,deDGEList-method | MA-like plot for deDGEList objects |
quantileAdjust | Normalizes a dataset by using a quantile adjustment |
readDGE | Read a list of files containing DGE data |
show,deDGEList-method | differential expression of Digital Gene Expression data - class |
show,DGEList-method | Digital Gene Expression data - class |
show,EBList-method | differential expression of Digital Gene Expression data - class |
tau2.0.objective | Objective function for tau2 |
topTags | Displays the top differentially expressed tags in a table |