Question: processing Illumina HT12v4.0 expression data from GEO
gravatar for Abhi
4.8 years ago by
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



illlumina bioconductor R • 1.9k views
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