Why does taply take the subset as NA and not exclude them totally
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I have a question. I want to make a barplot with the mean and errorbars, where it is grouped for two factors. To get the mean and the standard errors I used the function tapply.  

However for one of the factor I want to drop one level. 

So what I did was did: 

dataFE<-data[-which(plant=="FS"),] -> this works fine, I get exactly the data set I want without the FS level of the factor plant 

Then to get the mean and standard error I use this: 

means<-with(dataFE,as.matrix(tapply(leaves,list(plant,Orchestia),mean),nrow=2)

e<-with(dataFE,as.matrix(tapply (leaves,list(plant,Orchestia),function(x)
  sd(x)/sqrt(length(x))),nrow=2))

And there something strange happens, it does not calculate the FS, however it puts it in a table with NA: 

 	row.names	no	        yes
1	F	        7.009022	5.307185

2	FS	        NA	        NA

3	S	        2.837139	2.111054

This I don't want, cause if I use this in barplot2 (package gplots) then I will get an empty bar for the FS, whereas that one should not be there at all. 

So does any of use have a solution or an other method to get a nice barplot :). Thanks any way! 


