Nothing
cq2genorm <-
function(data,genes,effic,noamp=38) {
ngenes=length(genes)
for (g in genes) {
if ((g %in% effic[,1])==FALSE) {
stop(paste("missing efficiency for ",g,sep=""))
}
e=effic[effic[,1]==g,2]
if (length(which(data[,g]==(-1))>0)) {
warning(paste("Warning: ", length(which(data[,g]==(-1))), " no-amplification instances for gene ",g,"; these will be converted to Cq=",noamp,sep=""))
data[which(data[,g]==(-1)),g]=noamp
}
ii=which(!is.na(data[,g]))
data[ii,g]=data[ii,g]*log(e)*(-1)
}
c=data[,genes]
for (g in names(c)){
c[,g]=c[,g]-mean(c[,g],na.rm=T)
}
# removing rows with NAs
c.nona=data.frame()
for (r in c(1:length(c[,1]))){
if (sum(is.na(c[r,]))) next
c.nona=data.frame(rbind(c.nona,c[r,]))
}
return(exp(c.nona))
}
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