Normal Uniform Differential Gene Expression detection


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Documentation for package ‘nudge’ version 1.44.0

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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