# Normal Uniform Differential Gene Expression detection

## Documentation for package `nudge' version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

hiv | Microarray intensity expression levels for HIV type 1 infection of CD4+ T-Cell lines
like | Microarray intensity expression levels for like-like data
neg.contr | Indicator of known truly non differentially expressed genes in the hiv dataset
norm1a | Function for normalizing the mean of single replicate log ratios
norm1b | Function for normalizing the mean and variance (or just the variance) of single replicate log ratios
norm1c | Function for normalizing the mean of average-across-replicates log ratios
norm1d | Function for normalizing the mean and variance of average-across-replicates log ratios
norm2c | Function for normalizing the mean of average-across-replicates log ratio differences
norm2d | Function for normalizing the mean and variance of average-across-replicates log ratio differences
nudge1 | Function for normalizing data, fitting a normal-uniform mixture and estimating probabilities of differential expression in the case where the two samples are being compared directly
nudge2 | Function for normalizing data, fitting a normal-uniform mixture and estimating probabilities of differential expression in the case where the two samples are being compared indirectly through a common reference sample
pos.contr | Indicator of known truly differentially expressed genes in the hiv dataset