R/filterWellAboveSIGNALv2.R

In AgiMicroRna: Processing and Differential Expression Analysis of Agilent microRNA chips

`filterWellAboveSIGNALv2` <-
function(flag,GErep,nGE,Limit,limNEG) {

        index=0
        ii=0
        while(ii < nGE) {
        ii=ii+1
        minSize=length(which(GErep == unique(GErep)[ii]))*(limNEG/100)  
        pos=which(GErep == ii) 
                                
        aux=flag[pos]
        nan=!is.na(aux)        
        aux=aux[nan]            
        lp=length(aux)          

                sumSNR=0
                jj=0
                while(jj < lp ){
                jj=jj+1

                        if(aux[jj] >= Limit[pos[jj]]){
                        sumSNR=sumSNR+1
                                if(sumSNR >= minSize){
                                index=1
                                jj=lp + 1  # exit the while(jj)
                                ii=nGE +1  # exit the while(ii)
                                }
                        }
                }
         }    
	return(index)
} # end of function