R: for-loop with ddply

Question

I'm new to R and to stackoverflow so I'm sorry if the question or it's format isn't ideal...

I'm trying to get some basic statistics from a matrix by using ddply and I wanted to make a process a bit faster by using for -loop. Unfortunately this wasn't as easy as I had thought...

Strain  gene1         gene2      gene3  .   .   .
 A    2.6336700     1.42802     0.935742
 A    2.0634700     2.31232     1.096320
 A    2.5798600     2.75138     0.714647
 B    2.6031200     1.31374     1.214920
 B    2.8319400     1.30260     1.191770
 B    1.9796000     1.74199     1.056490
 C    2.4030300     1.20324     1.069800
 .
 .
 .
----------

for (n in c("gene1","gene2","gene3","gene4")) {
  summary <- ddply(Data, .(Strain), summarise,
                mean = mean(n),
                sd   = sd(n),
                se   = sd(n) / sqrt(length(n)) )
}

In results it reads that mean = 6 and both sd and se are "NA" ... obviously not what I had in mind.

If I get rid of the for -loop and manually insert the column name ("gene1"):

summary <- ddply(Data, .(Strain), summarise,
              mean = mean(gene1),
              sd   = sd(gene1),
              se   = sd(gene1) / sqrt(length(gene1)) )

Now it seems to give me the correct result. Can someone enlighten me on this matter and tell me what I'm doing wrong?

Answer 1

I know you didn't ask for it, but here is a solution with aggregate in base.

# One line in base.
aggregate(Data[paste0('gene',1:3)],by=Data['Strain'],
     function(x) c(mean=mean(x),sd=sd(x),se=sd(x)/sqrt(length(x))))