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On Jul 16, 2010 2:32 PM, "Wolfgang Huber" <whuber@embl.de> wrote:

Ning

I assume you are refering to the normalizePlates function in the cellHTS2
package. (Please don't forget in the future to provide such information, and
also sessionInfo(), this is much better than letting us guess.)

There are two answers to your question:

1. You can use the 'assayData' accessor to read from or write to the data
slot. For instance:

library("cellHTS2")
datadir = system.file("KcViabSmall", package = "cellHTS2")
x = readPlateList("Platelist.txt", "KcViabSmall", path=datadir)

class(x)
ls(assayData(x))
head(assayData(x)$"Channel 1")

if(storageMode(assayData(x))=="lockedEnvironment")
   storageMode(assayData(x)) = "environment"

assayData(x)$"Channel 1" = assayData(x)$"Channel 1" * pi/2

/* Background: The function 'normalizePlates' takes an object of class
'cellHTS2' with raw readings as input and returns one with normalised data
as a result. The class 'cellHTS2' derives from 'NChannelSet', which is a
common Bioconductor class for matrix-like data plus all relevant metadata.
*/

2. You can have a look at the source code of 'normalizePlates' (which is
simply a wrapper to call one of the specific normalization methods selected
by the argument "method") and copy/edit it to a new function that calls your
favorite normalization function instead.

       Best wishes
       Wolfgang





On Jul/8/10 10:08 PM, Ning wrote:
>
> Hi everyone,
>
> The cellHTS2 method normalizePlates has n...
-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber



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