col_ordering = c(9,10,7,8)#KO_M1vsM2
poly =poly0[,col_ordering];
poly = poly[(rowSums(poly[,1:2])>=2)&(rowSums(poly[,3:4])>=2),]
conditions = factor(c("IFN","IFN","IL4","IL4"));
exp_study = DGEList(counts=poly, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study)
tTags = topTags(et,n=NULL,adjust.method = "fdr")
1r <- rownames(tTags)
c=cpm(exp_study)[r, order(exp_study$samples$group)]
x=merge(x=as.data.frame(tTags),y=gl,by="row.names",all.x=TRUE)
x=x[,!(names(x) %in% "ID")]
rownames(x)=x$Row.names;
x=x[,!(names(x) %in% "Row.names")]
x2=merge(x=x,y=c,by="row.names",all.x=TRUE)
x=x2[,!(names(x2) %in% "ID")]
x=cbind(x,1000*x[,8]/x$genelength,1000*x[,9]/x$genelength,1000*x[,10]/x$genelength,1000*x[,11]/x$genelength)
x=cbind(x,0.5*(x[,12]+x[,13]),0.5*(x[,14]+x[,15]))
write.table(x, file="edgeRgenesPolyExpr-KO_M1vsM2.csv")
x_m2=x
for (i in 8:11){
  print (colnames(x)[i])
  tt=summary(x[,i]>0)
  print(tt)
}

str(exp_study$counts)
 int [1:21866, 1:4] 5 10 3 2 1 0 2 2 11 2 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:21866] "ENSMUSG00000051951" "ENSMUSG00000103377" "ENSMUSG00000104017" "ENSMUSG00000103025" ...
  ..$ : chr [1:4] "KO_IL4_replicate_IIb" "KO_IL4_replicate_Ib" "KO_IFN.gamma_replicate_IIb" "KO_IFN_replicate_Ib"
col_ordering = c(9,10,7,8)#KO_M1vsM2
poly =poly0[,col_ordering];
poly = poly[(rowSums(poly[,1:2])>=2)&(rowSums(poly[,3:4])>=2),]
conditions = factor(c("IFN","IFN","IL4","IL4"));

col_ordering = c(9,10,7,8)#KO_M1vsM2
poly =poly0[,col_ordering];
poly = poly[(rowSums(poly[,1:2])>=2)&(rowSums(poly[,3:4])>=2),]
conditions = factor(c("IL4","IL4","IFN","IFN"));
exp_study = DGEList(counts=poly, group=conditions);exp_study = calcNormFactors(exp_study);exp_study = estimateCommonDisp(exp_study);exp_study = estimateTagwiseDisp(exp_study);et = exactTest(exp_study,pair=c("IFN","IL4"))
tTags = topTags(et,n=NULL,adjust.method = "fdr")

Comparison of groups:  IL4-IFN 
                           logFC    logCPM       PValue          FDR
ENSMUSG00000020641 -5.8099539420 11.226557 1.736083e-40 3.004988e-36
ENSMUSG00000022126 -6.2315874981  9.663629 2.748548e-40 3.004988e-36
ENSMUSG00000020638 -5.5310326460  9.361139 2.561904e-34 1.867286e-30

poly[rownames(poly)=="ENSMUSG00000020641",]
                   KO_IL4_replicate_IIb KO_IL4_replicate_Ib
ENSMUSG00000020641                   47                  81
                   KO_IFN.gamma_replicate_IIb KO_IFN_replicate_Ib
ENSMUSG00000020641                       4046                6115