example code:
P = function(whichday,columns){
y = which(pvalue[,whichday]<Pvaluetest, arr.ind=TRUE)
dayarb = raw_urine[y,day1_ind]
daystand = raw_urine[y,columns]
meandayxx = geometricmeanRow(dayarb)
meandayyy = geometricmeanRow(daystand)
diff = meandayyy - meandayxx
for(i in 1:nrow(diff)){
if(diff[i]>0){
#diffbig = meandayxx<meandayyy
x_index[i] = which(diff[i]>0)
x[i] = raw_urine[x_index[i],1]
dayx[i]= raw_urine[x_index[i],day1_ind]
dayy[i] = raw_urine[x_index[i],columns]
jpeg("test 1.jpg",width=800, height = 800)
matplot(x[i],dayx[i],lwd = 3,pch=1,col = "black",xlim=xbound, ylim=ybound)
matpoints(x[i],dayy[i],lwd=3,pch=1,col="red")
dev.off()
return(length(y),length(x_index),diffbig)}
else{
xx_index[i] = which(diff[i]<0, arr.ind=TRUE)
xx[i] = raw_urine[xx_index[i],1]
dayxx[i] = raw_urine[xx_index[i],day1_ind]
dayyy[i] = raw_urine[xx_index[i],columns]
jpeg("test 2.jpg",width=800, height = 800)
matplot(xx[i],dayxx[i],lwd = 3,pch=1,col = "black",xlim=xbound, ylim=ybound)
matpoints(xx[i],dayyy[i],lwd=3,pch=1,col="red")
dev.off()
return(length(xx_index))}}}

I ran this code and I got "Error in 1:nrow(diff) : NA/NaN argument". I this
my problem is with the way I define the i index with the rest of the
functions.
Basically I want to run for every row of the matrix that is called the
"diff". without the for loop, I don't know how to make it work but with it,
I have a lot of bugs in there that hopefully someone can just point out a
general direction.
Thank you very much!

-- 
Edward Chen
Email: edchen51@gmail.com
Cell Phone: 510-371-4717

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