pickprobes.R.txt

probes                                  <- read.table("HuGene-1_0-st-v1.hg19.probe.tab", header=T, sep="\t")
probes                                  <- probes[-which(probes$category == "category"),]
probes$Probe.ID 			<- as.numeric(levels(probes$Probe.ID)[probes$Probe.ID])
probes$Transcript.Cluster.ID		<- as.numeric(levels(probes$Transcript.Cluster.ID)[probes$Transcript.Cluster.ID])
probes$probe.x 				<- as.numeric(levels(probes$probe.x)[probes$probe.x])
probes$probe.y 				<- as.numeric(levels(probes$probe.y)[probes$probe.y])
probes$assembly 			<- as.factor(as.character(probes$assembly))
probes$seqname 				<- as.factor(as.character(probes$seqname))
probes$start[which(probes$start=="---")]<- NA
probes$start				<- as.numeric(levels(probes$start)[probes$start])
probes$stop[which(probes$stop=="---")]	<- NA
probes$stop 				<- as.numeric(levels(probes$stop)[probes$stop])
probes$strand 				<- as.factor(as.character(probes$strand))
probes$probe.sequence			<- as.character(probes$probe.sequence)
probes$target.strandedness		<- as.factor(as.character(probes$target.strandedness))
probes$category             		<- as.factor(as.character(probes$category))

probes					<- probes[-which(probes$category=="rescue->FLmRNA->unmapped"),]
probes					<- probes[-which(probes$category=="control->bgp->antigenomic"),]
probes					<- probes[-which(probes$category=="normgene->exon"),]
probes					<- probes[-which(probes$category=="normgene->intron"),]
probes 					<- probes[-which(probes$Probe.ID %in% subset(probes, category=="control->affx")$Probe.ID),]

probes					<- probes[,c(1,2,10)]
tmp					<- table(as.factor(probes$Probe.ID))
probes_unique 				<- subset(probes, ! Probe.ID %in% as.numeric(unlist(dimnames(tmp[tmp>1]))))

tmp<-table(as.factor(probes_unique$Transcript.Cluster.ID))
probes_worthy<-subset(probes_unique, Transcript.Cluster.ID %in% as.numeric(unlist(dimnames(tmp[tmp>3]))))
write.table(probes_worthy[,1:2], file="../opt-microarray/probe_selection/probes_worthy.tab", row.names=F, sep="\t")