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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
Thanks!
-Abhi