detectionPnegNormGS {sesame} | R Documentation |
The function takes a SigSet
as input, computes detection p-value
using negative control probes parametrized in a normal distribution a la
Genome Studio and returns a new SigSet
with an updated mask slot.
detectionPnegNormGS(sset, pval.threshold = 0.05, return.pval = FALSE)
sset |
a |
pval.threshold |
minimum p-value to mask |
return.pval |
whether to return p-values, instead of a
masked |
P-value is calculated using negative control probes as the estimate of background where Grn channel and Red channel are merged. But when estimating p-value the Red and Grn are summed (non-ideal).
detection p-value
sset <- sesameDataGet("HM450.1.TCGA.PAAD")$sset sum(mask(sset)) sset_with_mask <- detectionPnegNormGS(sset) sum(mask(sset_with_mask))