Question: Normalization
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9.2 years ago by
Ning80
Ning80 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
normalization cellhts2 • 527 views
modified 9.2 years ago by Wolfgang Huber13k • written 9.2 years ago by Ning80
0
9.2 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k 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 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber