[BioC] Filtering Affymetrix data. (Newbie)

James MacDonald jmacdon at med.umich.edu
Wed Aug 27 10:56:18 MEST 2003

You access the data by using the pm() and mm() functions.

For instance:

pm(abatch)[1:1000] <- 200

will replace the first 1000 pm values with 200.



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

>>> Marcus <marcusb at biotech.kth.se> 08/27/03 03:59AM >>>
Hello all!!

How do I get access to the individual probe intensities in my data object 
(which I get with the
data<-ReadAffy() command) ?

I know that I can get them with the mm() and pm() functions but if I would 
like to see,filter,remove or change the data in the data object, how is 
this accomplished?

Essentially: How is the data object built up and how do you access it??

Another question: How and where is the background value stored/calculated??


Marcus Gry Björklund

Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
Department of Molecular Biotechnology
106 91 Stockholm, Sweden

Phone (office): +46 8 553 783 39
Fax: + 46 8 553 784 81
Visiting adress: Roslagstullsbacken 21, Floor 3
Delivery adress: Roslagsvägen 30B

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