[BioC] lumi and Affy bgadjust

[Simon Lin]

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


***************************************************
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
>>
>>
> 
> 
>