[BioC] lumi and Affy bgadjust

parantu shah parantu.shah at gmail.com
Mon Sep 21 16:13:28 CEST 2009


Hi.

I am using Lumi package for analyzing Illumina gene expression array
data. I don't have control data and I am using sample probe
profile.txt file.

 I use 'force positive' and 'bgAdjust.affy' options to do background
correction. After doing VST and RSN normalization - estimate of differentially
expressed genes (using limma)  is very different (1675 vs. 1134).

I am attaching you the box plot of VST data after no correction,
forcepositive and bgAdjust.affy in a hope that it will be useful to
you in answering.

I would also appreciate any other suggestions you have.

Thanks and best regards,
Parantu.


--
Parantu Shah, PhD
Dept. of Biostatistics & Computational Biology
Dana-Farber Cancer Institute
Harvard School of Public Health

CLS-11075,  3 Blackfan Circle
Boston MA 02115
Phone : 617 582 8852
http://www.hsph.harvard.edu/~pshah



-- 
Parantu Shah, PhD
Dept. of Biostatistics & Computational Biology
Dana-Farber Cancer Institute
Harvard School of Public Health

CLS-11075,  3 Blackfan Circle
Boston MA 02115
Phone : 617 582 8852
http://www.hsph.harvard.edu/~pshah
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