[BioC] lumi and Affy bgadjust

Pan Du dupan at northwestern.edu
Mon Sep 21 19:01:46 CEST 2009

Hi Parantu

The boxplot looks for me. Because of the higher variation in the low
expression range, VST transformation shrinks the values in this region,
which is also reflected in the boxplot. A following up normalization is
required after VST transformation. As for which normalization method to use,
it also depends on the data set and the purpose of the study.
Hope this is helpful to you.


On 9/21/09 9:13 AM, "parantu shah" <parantu.shah at gmail.com> wrote:

> 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

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