processing Illumina HT12v4.0 expression data from GEO
Entering edit mode
9.9 years ago
Abhi ★ 1.6k

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 R bioconductor • 3.1k views

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