Help with the choice of the Affymetrix normalization method

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Help with the choice of the Affymetrix normalization method

Postby Fitoedu » Jan 29 2010 8:12 am

Hello,
I am a PhD student.
I have trouble choosing what the best method of normalization of my arrays.

I am using the Affymetrix Barley array 22k, I have 6 arrays hybridized, 3 control and three treated. The parameters of RNA and hybridization are correct.
By normalizing the arrays each normalization method gives a different result when applying the statistics.
I'm using GeneSpring and GEPAS for the analysis, none of these programs gives me a good indication of what is the best method of normalization, all of the Box-Plots very similar.

Could someone show me software to determine which is the best method of normalization, a manual or protocol decisions.

Thanks a lot
Fitoedu
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Re: Help with the choice of the Affymetrix normalization method

Postby stylothecancer » Jan 31 2010 3:57 am

Hi Fitoedu,

Normally, Quantile normalization after choosing RMA sumarization and baseline transformation to median of all sample works fine for my Affymetrix data.
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Re: Help with the choice of the Affymetrix normalization method

Postby Fitoedu » Feb 01 2010 1:01 pm

Hi stylothecancer,

Thank you very much for the reply. The RMA method using the controls to generate the baseline works well, but I get very few genes compared with other analysis. I am considering using the RMA analysis with reference but complement them with data obtained by LiWong normalization .
Think it's a good idea? Since I get in RMA genes are represented in which I have used Li Wong.
Thanks for your answer.
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