Gene expression data normalization by family pedigree
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gt2260 • 0
@gt2260-9843
Last seen 8.1 years ago

Hi,

I have an family expression dataset and I need to conduct normalization of my .CEL files within each family instead that for the overall sample.

Is there a specific feature that applies the rma by levels of "wafer" (as when we perform the MA plot group vs group)?

 

thank you

oligo • 517 views
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@james-w-macdonald-5106
Last seen 3 hours ago
United States

No, there isn't a way to do that (aside from running rma on subsets of the samples), and it really doesn't make sense to do it anyway. The normalization and summarization steps of the RMA algorithm are intended to eliminate as much technical variability while retaining biological variability. Accounting for intra-family correlations should happen at the modeling stage, not at the preparation stage.

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