Normal Uniform Differential Gene Expression detection

Documentation for package ‘nudge’ version 1.44.0

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