Question: Affy normalization and filtering method
gravatar for Juliet Hannah
8.5 years ago by
Juliet Hannah360
United States
Juliet Hannah360 wrote:
All, I am reading through and I am not understanding the methods section regarding the preprocessing and normalization. The authors write: For Affy Hu6800 and U133 microarrays, we threshold at 20 and 100,000 units. Gene filtering excludes genes with less than 5-fold and 500 units of maximum difference for the first leukemia example, 8-fold/800 for the second leukemia example, and 3-fold/300 for the lung. We rank the genes according to their expression levels and replace the value by 10,000 X (rank(gene) - 1)/(number of genes - 1). Is this a common approach? Could anyone point me to any references regarding this, and especially how to conduct this using Bioconductor. Of course, it does not seem complex, but I just don't follow the description. Thanks for your help. Regards, Juliet Hannah
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