Question: How to apply RLM normalization to a protein expression matrix in R?
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gravatar for tasjfasfankihj
6.0 years ago by
tasjfasfankihj
tasjfasfankihj10 wrote:

I have a combined dataset of 123 samples and 9,482 features (expression levels of antibodies from Invitrogen's ProtoArray v5.0).  Based on (http://archive.gersteinlab.org/papers/e-print/rlm/preprint.pdf), RLM normalization is the optimal method for my data.  What I need help with is figuring out how to implement it in R.

PAA package says it has it, but doesn't work and the only thing I can find online about it is someone's post asking for help with no response.

Is there a way to do it with Limma's normalizebetweenarrays()?

The authors of the article I linked above apparently used the MASS package, but I haven't been able to figure out how.

Can someone please explain how to do it? Example code would be really helpful if possible.

rlm normalization R • 2.0k views
ADD COMMENTlink modified 6.0 years ago by Mo920 • written 6.0 years ago by tasjfasfankihj10
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gravatar for Mo
6.0 years ago by
Mo920
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Mo920 wrote:

I have never done this normalisation , have a look at this package , I found there is a function for RLM normalisation (page 8) http://bioconductor.org/packages/release//bioc/manuals/PAA/man/PAA.pdf

You can find some theory here 

http://www3.it.nuigalway.ie/agolden/bioconductor/version1/MicroArrayAnalysis.pdf

here is an example of RLM in MASS package 

https://stat.ethz.ch/R-manual/R-devel/library/MASS/html/rlm.html

Page 127 of this as well 

http://cran.r-project.org/web/packages/MASS/MASS.pdf

Hope it helps 

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by Mo920
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