Talk:FirstPrinciples.R

Hi Vinoy,

It's better to keep the discussions on the list for other users that may 
have the same question. If they are not evenly spaced, after the 
normalizations you can rearrange the MA object so that they are evenly 
spaced, at least the 90% that are spotted twice. The ones that are spotted 
26 times are likely some sort of control spots, and you can probably safely 
ignore them. Why are some spotted three times? If you want to keep these 
genes in, a quick-and-dirty solution would be to just pick two of the three 
spots. The following code *should* work to rearrange the order of the 
genes, then pick out the first two spots for each unique ID.

MA.norm <- MA.norm[order(MA.norm$genes$ID),]

x <- unique(MA.norm$genes$ID)

MA.norm$genes$spotrep <- NULL

# I'm sure there's a better, faster way to do the following, but this is 
the only way I know how:

for (i in 1:length(x)) {
     y <- which( MA.norm$genes$ID == x[i] )
     MA.norm$genes$spotrep[y] <- 1:length(y)
     }

MA.norm.2spot <- MA.norm[MA.norm$genes$spotrep <= 2 , ]
# now your spacing=1 and ndups=2

HTH,
Jenny

Alternative approach:

sort(unlist(tapply(1:10, rep(1:2, each=5), sample,2)))