###do spatial correction for four line gDNAs
setwd ("final")
load ("attile1V7anno.RData")
source("readcel.R")
library(affy)

array.size <- 2560
probe.ok <- matrix(FALSE, nr=array.size, nc=array.size)
probe.ok.chrom <- matrix(NA, nr=array.size, nc=array.size)
probe.ok.position <- matrix(NA, nr=array.size, nc=array.size)
probe.ok[cbind(attile1$xpos+1, attile1$ypos+1)] <- TRUE
probe.ok.chrom[cbind(attile1$xpos + 1, attile1$ypos+1)] <-attile1$chr
probe.ok.position [cbind(attile1$xpos + 1, attile1$ypos+1)] <- attile1$bpstart

probe.ok.chrom.valid <- probe.ok.chrom[probe.ok]
probe.ok.position.valid <- probe.ok.position [probe.ok]
chrom.order <- order(probe.ok.chrom.valid, probe.ok.position.valid)


setwd ("../CEL/gDNA")
cel.files <- list.celfiles() 
mprobe.mean <- readcel (cel.files=cel.files, probe.number=nrow(attile1), array.size=2560, filter.size=81)

setwd ("../../final1")
save( mprobe.mean, file="gDNA.sc.RData", compress=T)
q("no")




### do quantile normalization and SFP detecton by siggenes
setwd ("final")
load ("gDNA.sc.RData")
library (affy)
library (siggenes)

gDNA.nq <- normalize.quantiles(mprobe.mean)
save (gDNA.nq, file="gDNA.sc.nq.RData", compress=T)

cl<- c(1,1,1,1,0,0,0,0)
system.time( sam.out <- sam(gDNA.nq[, 1:8], cl, rand=123, p0=0.95))
save (sam.out, file="SFP.samout.RData", compress=T)

summary(sam.out, seq(0.5, 1, 0.05) )
plot(sam.out, 0.95)
q("no")


   Delta   p0     False Called    FDR cutlow cutup    j2      j1
1   0.50 0.95 18745.571 150703 0.1182 -1.656 1.142 14934 1547852
2   0.55 0.95 14251.714 142660 0.0949 -1.752 1.203 11741 1552702
3   0.60 0.95 10963.486 135922 0.0766 -1.843 1.263  9479 1557178
4   0.65 0.95  8604.243 130229 0.0628 -1.928 1.322  7854 1561246
5   0.70 0.95  6873.671 125043 0.0522 -2.009 1.381  6662 1565240
6   0.75 0.95  5633.714 120253 0.0445 -2.087 1.440  5712 1569080
7   0.80 0.95  4727.814 115840 0.0388 -2.162 1.499  4979 1572760
8   0.85 0.95  4072.014 111858 0.0346 -2.237 1.558  4359 1576122
9   0.90 0.95  3579.129 107935 0.0315 -2.310 1.617  3820 1579506
#10  0.95 0.95  3205.557 104154 0.0292 -2.382 1.676  3397 1582864
11  1.00 0.95  2920.586 100580 0.0276 -2.451 1.734  3059 1586100



  Delta   p0    False Called    FDR cutlow cutup    j2      j1
1  0.50 0.95 18745.57 150703 0.1182 -1.656 1.142 14934 1547852
2  0.51 0.95 17734.29 148925 0.1131 -1.677 1.154 14127 1548823
3  0.52 0.95 16790.03 147335 0.1083 -1.695 1.167 13522 1549808
#4  0.53 0.95 15891.06 145729 0.1036 -1.713 1.179 12950 1550842
5  0.54 0.95 15052.57 144188 0.0992 -1.733 1.191 12308 1551741
6  0.55 0.95 14251.71 142660 0.0949 -1.752 1.203 11741 1552702


6  0.45 0.95  24947.24 161374 0.147 -1.545 1.082  20285 1542532




























