processing Illumina HT12v4.0 expression data from GEO
0
0
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

Thanks!

-Abhi

illlumina R bioconductor • 3.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 1336 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6