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[]
mat <- exprs(gse)
Appreciate any pointers
PS: cross posted on bioconductor mailing list