[BioC] Normalization of Intensities

Naomi Altman naomi at stat.psu.edu
Sun May 16 17:45:05 CEST 2004

You should probably use expresso, justRMA or gcrma to normalize these 
data.  You should be using the "affy" library, not the marray library.

If you really prefer loess and if the arrays are paired with one treatment 
and one control in each rep you can do the following:

M= log(trt)-log(ctrl)


You will get one normalized value for each gene for each rep.

To get more help on loess, just type "?loess", as I have not given you all 
the options.


At 04:07 PM 4/30/2004, E Motakis, Mathematics wrote:
>I am a rather new user of Bioconductor and I have one question. Which 
>function should I use to "loess" normalize gene intensities from an 
>experiment conducted with AFFYMETRIX? The experiment contains 3 replicates 
>with one treatment and one control condition for the genes.
>I cannot understand how I should use function "read.marrayRaw" if this is 
>the correct one.
>Thanks in advance.
>E Motakis, Mathematics
>E.Motakis at bristol.ac.uk
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

More information about the Bioconductor mailing list