Description Usage Arguments Value
The pipeline includes 1) quantile normalization 2) log-transformation of counts 3) combat batch correction 4) voom calculation of weights for testing from mean-variance relationship
1 2 |
counts |
Count matrix |
design |
model.matrix for differential expression testing |
batch |
factor indicating batch |
condition |
factor indicating biological condition |
lib.size |
library sizes, if NULL or missing, uses the sum of quantile-normalized counts (default=NULL) |
verbose |
print extra information |
plot |
plot the mean-variance fit |
filter |
filter genes with low expression |
... |
pass arguments to internal functions |
list with components elist (result of calling voom) and combatEstimates (batch effect estimates from combat)
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