[BioC] Affy: gene filtering before or after normalization??

Jing Shen Jing.Shen at UTSouthwestern.edu
Thu Oct 9 12:53:45 MEST 2003


I am going to work on affymetrix data analysis using Bioconductor Affy
package. In my understanding, the procedure for data analysis should be:
(1) import data (CEL files)
(2) data filtering ?? --- get rid of bad or false intensities (e.g.,sth
like filtering on flags, present or absent or expression values in
(3) data normalization --- several different methods based on probe cell
level or probe set level...
(4) now you have the data for statistical analysis...
I am wondering if anybody can give me some suggestions on data filtering
before (or after??) my data normalization if I use RMA() or expresso()?
Or what kind of gene filtering criteria do you guys use? or I don't need
to do that at all?


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