[BioC] Normalization

[Wolfgang Huber]

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 not the proper way for me to normalize
> my raw data, because I set up two criteria: one is used for measuring high
> signaling activity; the other is used for no activity measurement. Then I
> calculated the percentage of cells belonging to the part of high activity and
> also the percentage of cells in no activity part. So I used the percentage as
> my normalization method. Then I want to put the normalized results into
> cellHTS2. However I cannot find a way to import them in. It seems like the
> cellHTS2 only allows importing the raw data.
>
> Can anyone help?
>
> Thanks
> Ning
>
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-- 


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