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
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