negbead selection

[snewhouse]

## get neg control data from eset_bg
negativeControl <- getControlData(eset_bg)
negativeControl <- subset(negativeControl, negativeControl$controlType=="NEGATIVE")
negativeControl <- negativeControl[,c(3:dim(negativeControl)[2])]

## get neg control info mean,sd,max etc
neg_max <- apply(negativeControl,2,max)
neg_sd <- apply(negativeControl,2,sd)
neg_mean <- apply(negativeControl,2,mean)
neg_2sd <- neg_mean + 2*neg_sd

## sweep through gx matrix to id probes greater than Mean of negative beads
## rows are probes, cols are samples 

## THIS IS THE MAIN PROBE DETECTION CALCULATION
det <- sweep(gx, 2, round(neg_mean,2),">")