How is microarray normalization done in PIANO?
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@rfes-12351
Last seen 22 months ago
Spain

In the vignette, the authors talk about the normalization of microarray data from .CEL files to gene expression, followed by quality control. However, it is unclear how the normalization is done, including in their article in NAR. Does anyone know how this is done?

Thanks in advance.

R

piano microarray • 1.3k views
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@james-w-macdonald-5106
Last seen 23 hours ago
United States

In the vignette it says this on page 6:

The loadMAdata function will normalize the raw data (by default using the plier algorithm)

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To extend this answer slightly: ?loadMAdata returns information regarding this (see the normalization argument):

normalization - character string giving the normalization method, can be either "plier", "rma" or "mas5". Defaults to "plier".

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