subset an expression dataset by extracting genes based on their level of variation

VERBOSE(v, ...)

Arguments

dat

an expressionSet object

score

type of variation measure to use (can be 'mad', 'sd', or 'cv')

dir

direction of the gene ranking ('top': highest varying genes; 'bottom': lowest varying genes)

transform

transform the data before measuring variation

ngenes

number of top (or bottom) genes to extract

do.plot

plot the center vs. scale plot with selected genes highlighted

do.log

indicates whether to log the "x", "y", or "xy" axes, or "" none

Value

the filtered expressionSet object

Examples

# select the top 100 genes by median absolute deviation (mad) and also generate plot # Use example data, for data set information: ?eSet.brca.100 data(eSet.brca.100)
#> Warning: data set ‘eSet.brca.100’ not found
variationFilter(eSet.brca.100,score='mad',ngenes=50,do.plot=TRUE)
#> Error in nrow(dat): object 'eSet.brca.100' not found