[BioC] lumi and Affy bgadjust

Simon Lin S-Lin2 at northwestern.edu
Mon Sep 21 19:43:15 CEST 2009

Hi Parantu,

As Dr. Du said, the background correction, transformation, and 
normalization steps have a complex impact on the end-results.

There are a few publications (NAR) on the topic of background 
correction, but I think further research is still necessary.

If you are interested in a follow up investigation, we would certainly 
be happy to facilitate.

Best regards,


Simon Lin, MD, CSDP
Director of Bioinformatics Consulting
750 N. Lake Shore Drive, 11th Floor, Room 174
Research Associate Professor
Northwestern University Biomedical Informatics Center/NUCATS
Chicago, IL  60611
S-Lin2 at northwestern.edu
Phone 312-503-2353
Fax 312-503-5388

> 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.
> Pan
> 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

More information about the Bioconductor mailing list