Re:Normalization in r

Question

[ash]

Hello to everyone,

I have a question regarding normalization in microarray data. I would like to normalize my training set using rma. After normalizing my training set, I would like to use the training set parameters(mean,sd) to normalize my test set. Is there any function to normalize my test using training set parameters. Or just use the formula like (test-mean(train))/sd(train). It would be really helpful if you solve my problem. Thanks in advance

Answer 1

[cpad0112]

see if this package in R helps you out: www.bioconductor.org/packages/release/bioc/html/RefPlus.html

from the vignette, copy/pasted:

The RMA+ algorithm calculates the microarray intensities using a pre-stored RMA model trained on a reference microarray set (can be standard reference microarrays, microarrays from an independent study, or an incomplete set of microarrays in a study)

Answer 2

[Sean Davis]

You may want to consider fRMA (frozen RMA) as a general solution:

https://www.bioconductor.org/packages/release/bioc/html/frma.html