Question: RMA normalization in XPS
0
gravatar for dhwani.dholakia
5.8 years ago by
United States
dhwani.dholakia0 wrote:

I want to normalize my affymetrix data which has more than 5000 .CEL files. since the system doesnot support these many files, i want to normalise my gene expression(.CEL)  files using XPS

Now to normalise a file in xps we have to perform certain steps

1) Import additional CEL files into a DataTreeSet and update ROOT data file.

2) preprocess raw data

I am not able to understand on how create a root schema for my .CEL files

xps R • 1.5k views
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by dhwani.dholakia0

Maybe, if you give us more relevant details.

ADD REPLYlink written 5.8 years ago by _r_am32k

I have .CEL files of 17 GB and i want to do RMA normalization. can you please tell me on how to proceed

The tutorial of xps seems very complicated

ADD REPLYlink written 5.8 years ago by dhwani.dholakia0

Add these details to your question using the option to edit post. And it will also help your cause if you pointed to exact parts of the xps tutorial where you face difficulties.

I do not have any experience with RMA normalization, but those that do will be more inclined to help you if you invest some time explaining your premise and your problem.

ADD REPLYlink written 5.8 years ago by _r_am32k

## first, load ROOT scheme file and ROOT data file

scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))

data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

data.rma <- rma(data.test3,"tmp_Test3RMA0",tmpdir="",background="pmonly",normalize=TRUE,add.data=FALSE)

 

what does schema.test3 signifies. 

ADD REPLYlink written 5.8 years ago by dhwani.dholakia0

Please read through this to understand why how you're adding details does not help: http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1002202 . Pl give special note to rules 2 and 7.

And please note my statement "Add these details to your question using the option to edit post". Please edit your question so people do not have to read through comments to figure out what you're trying to solve.

ADD REPLYlink written 5.8 years ago by _r_am32k
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