# Cowpea 
# 12 slides
# ER3 analysis with F and R library

library(SSHscreen)

cowpeaSSH <- SSHscreen(path = "/Users/Nanette/SSHscreen/cowpea_F_and_R", source = "genepix", norm.plot = TRUE, mfrow = c(4,2), legend = TRUE,  bc.method = "normexp", wa.method  = "printtiploess", ba.method = "Aquantile", irregular = TRUE, ndups = 2, spacing = 1, spot.ave = FALSE, method = "ER3", toplist = "all", adjust = "fdr", negflags = 0, offset = 50, weights = TRUE, library = "both", sort = "p", cutoff = 0.05, proportion = 0.5)


write.table(cowpeaSSH$tt.ud.F,file="/Users/Nanette/SSHscreen/cowpea_F_and_R/cowpea$tt.ud.F.txt",sep="\t")
write.table(cowpeaSSH$tt.ar.F,file="/Users/Nanette/SSHscreen/cowpea_F_and_R/cowpea$tt.ar.F.txt",sep="\t")

write.table(cowpeaSSH$tt.ud.R,file="/Users/Nanette/SSHscreen/cowpea_F_and_R/cowpea$tt.ud.R.txt",sep="\t")
write.table(cowpeaSSH$tt.ar.R,file="/Users/Nanette/SSHscreen/cowpea_F_and_R/cowpea$tt.ar.R.txt",sep="\t")