[BioC] esApply puzzler

[Stephen Henderson]

I'm having a few problems with using esApply.

Simply I have my exprSey data split into groups.

e.g.

>pData(SE.exprs)

                            sample 	group
SE 100503.CEL           	1   	1
SE 240503.CEL       		2   	1
SE 100503.CEL           	3   	2
SE 240503.CEL       		4   	2
SE 100503.CEL            	5   	3
SE 240503.CEL        		6   	3
SE 100503.CEL          		7   	4
SE 240503.CEL      		8   	4

I want to use esApply and the dist function to calculate "maximum" distances
between any given group (for a simple filtering routine).


So..
>maxdiff<-function(x)
+	{
+ 	x<-as.data.frame(split(x,group))


## gives me a list object x like

$"1007_s_at"
                               cMSC     MAPC      MSC    rcMSC
SE cMSC 28f 100503.CEL     8.675171 8.607033 8.973225 8.805668
SE CMSC 40YMALE 240503.CEL 8.681846 8.578437 8.868079 8.509754
... etc.


## so then I wish to calculate the distances (max) between columns/groups 
+ dist(t(x),"maximum")}

## and use esApply to calculate it for each gene
>esApply(SE.exprs,1, maxdiff)

Error in array(ans, c(len.a%/%d2, d.ans), if (is.null(dn.ans)) { : 
        length of dimnames[1] not equal to array extent

# gives an error because it's a list-- obviously I can extract it using 
# t(x$1007_s_at) for the first case but how do I do this for each and every 
# case?

# or simply is their another function to coerce the vector x into a 
# data.frame  without going through a list. I hope that's clear!

Stephen Henderson
WIBR


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