[BioC] help with defining batch slot in cellHTS2

[Yan Zhou]

Hi, Ligia,


I'll need your help with defining the batch slot in cellHTS2 again.I run 
into problem and I think either there's a bug in the function code of 
cellHTS2 or I'm doing something extremely stupid here.

I have 76 plates(in 96 well format) in dulipate, and first 3 batch each 
has 20 plates within a batch(with duplicate, which means 40 plates total 
for each batch). my code to define the batch as follows: (regards to the 
description of the package I need to define a array with dimension of 
(96*76,2,1) to feed to "batch" function)

"DL" is my cellHTS object;

ind=c(rep(1:3,each=96*20),rep(4,96*16))
bt=array(rep(ind,2),dim=c(96*76,2,1)) #an array with dimensions 
'Features x Samples x Channels' (7296 x 2 x 1)
batch(DL) <- bt

but I got error message as follows,which is very confusing(asked me to 
build array with dimension of plate number,sample and channel):
 >Error in `batch<-`(`*tmp*`, value = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,  :
 'value' should be an array of integer values corresponding to the batch 
number for each plate, sample and channel!

So, I changed the array as suggested by the error message due to curiosity:

ind2=c(rep(1:3,each=20),rep(4,16))
bt2=array(rep(ind2,2),dim=c(76,2,1))
batch(DL) <- bt2

But then got error message as belows:

 >Error in `batch<-`(`*tmp*`, value = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,  :
 'value' should be an array with dimensions 'Features x Samples x 
Channels' (7296 x 2 x 1).


Which suggested I should use the code from the first block. I fell into 
a loop here, which I couldn't figure out what's wrong. Could you help to 
point out  to the right direction or give me some clues here?

thanks a lot.

yan