Question: How is microarray normalization done in PIANO?
gravatar for rfes
5 months ago by
rfes0 wrote:

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.


ADD COMMENTlink modified 5 months ago by James W. MacDonald46k • written 5 months ago by rfes0
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald46k wrote:

In the vignette it says this on page 6:

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

ADD COMMENTlink written 5 months ago by James W. MacDonald46k

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".

ADD REPLYlink written 5 months ago by Leif Väremo70
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