search for: s0vss24

...sign <- model.matrix(~0+TS) #write design object to text file write.table(design,file="design.txt",sep="\t",col.names=NA) colnames(design) <- levels(TS) #for eset put in your M values - see ?lmFit for object types fit <- lmFit(eSet, design) cont.matrix<-makeContrasts(s0vss24=s.0-s.24, s24vss48=s.24-s.48, s48vss96=s.48-s.96, c0vsc24=c.0-c.24, c24vsc48=c.24-c.48, c48vsc96=c.48-c.96, levels=design) write.table(cont.matrix,file="cont.matrix.txt",sep="\t",col.names=NA) # estimate the contrasts and put in fit2 fit2 <- contrasts.fit(fit, cont.matrix) fi...

...lumns. The first column that it does not read in is df.residual. fit2<-read.table(fit2, file="fit2.txt",sep="\t",quote="",comment.char="",as.is=TRUE) The first few lines of fit2.txt (does not include all 38 columns) looks like this: coefficients.s0vss24 coefficients.s24vss48 coefficients.s48vss96 coefficients.c0vsc24 coefficients.c24vsc48 coefficients.c48vsc96 df.residual sigma stdev.unscaled.s0vss24 U179971039 0.058663 0.087575 0.074886 0.099245 -0.18102 0.311904 20 0.176096 empty1 -0.1296 -0.09105 0.238859 -0.25477 0.063964 0.38619...