Question: processing Illumina HT12v4.0 expression data from GEO
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gravatar for Abhi
4.8 years ago by
Abhi1.5k
United States
Abhi1.5k wrote:

Hi Guys

I would like to know the basic analysis workflow for downloading and processing a Illumina HTV12 expression data from GEO. I have seen the beadArray vignette but not sure which normalization process to use.

 

For example with Affy datasets I normally download the raw data and normalize it with fRMA package to produce a final expression matrix of genes.

 

Here is some code but basically the final goal is to produce a normalized  expression matrix at genelevel.

 

library( GEOquery )

gse <- getGEO("GSE58037")

gse <- gse[[1]]

mat <- exprs(gse)

Appreciate any pointers

 

PS: cross posted on bioconductor mailing list

Thanks!

-Abhi

illlumina bioconductor R • 1.9k views
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