Dear all, I want to compute the average of the three blocks for each x-variable which is equal slide in the code below. How can I do that ? block x1 x2 x3 x4 x5 1 23 22 23 24 23 1 21 25 26 21 39 1 23 24 22 23 23 2 20 21 23 24 28 2 32 23 34 24 26 2 19 34 34 13 34 3 12 32 ยด 23 34 19 3 23 24 25 26 27 3 12 78 23 24 24 # read table of data for this slide=(x1) a<-read.table(file = slide[i],header=T,sep='\t',na.strings="NA") #length(a$ID) #Eleminate Neg. and Pos. controls from the dataset. The logical negation of the "%in%" function, #tells subset to only select those row where the "ID" column does not contain either "empty" or "none" new <- subset(a,!ID %in% c("empty","none"," ")) #length(new$ID) #new[1:20,c(1,4,5,9)] #five first columns give position identifiers, include a column with block layout=new[,1:5] layout[1:30,] #9th columns which give the median foreground =values of x-variables fg1=as.matrix(new[,9]) length(fg1) mean(fg1) # calculate the mean of x1 #### I try to do something like :########## block1=fg1[layout$Block==1,] block2=fg1[layout$Block==1,] block2=fg1[layout$Block==1,] average=(block1+block2+block3)/3 but it did not work. ################## How can i calculate the means of remaining x_variables? ######### Read data for the remaining slides =x2,x3,x4,x5 ########### for (i in 2:num.slides){ na1 <- strsplit(na[[i]][k],".txt") na2 <- strsplit(na1[[1]][1],"-") bat=na2[[1]][1] sli=na2[[1]][2] nslide <- cbind(nslide,as.numeric(sli)) # nslide is a vector giving the number of the slide in the batch # read table of data for this slide a<-read.table(file=slide[i],header=T,sep='\t',na.strings="NA") new<- subset(a,!ID %in% c("empty","none"," ")) # append FG data to the matrices containing the slides already read fg1=cbind(fg1,as.matrix(new[,9])) } colnames(fg1)=nslide fg<-data.frame(peptide=c(new$Name),fg1) fg <- edit(fg) ##### Another question : I have three graphs which are displayed one after one with a large space between them. Can I move these graph closer each other by making them bigger and how ? Below is the code that i have written for plotting the graphs. par(mfrow=c(3,1)) for (j in 1:3) { boxplot(split(pos$y[pos$Block==j],pos$Slide[pos$Block==j]), col="lightgray", cex=.65, outline=TRUE, main=paste("Positive Controls Block",j)) }
Thank you for your help, Regards, Yen [[alternative HTML version deleted]]
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