Hi,

Im doing annotation on this article: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38376

Ive read in the txt file in R studio, but i dont know how to normalize it.

Thanks,

Anna

Not sure which text file you are referring to, but if you just want to have a look at the data and start exploring it, the easiest thing would be to load it using GEOquery.

library(GEOquery)

data <- getGEO("GSE38376")[[1]]

Thank you. This one on the page: GSE38376_non-normalized.txt

I want to do a QC and to get a gene list of diferencialy expressed genes

but ive never used illumina just affymetrix

I'm pretty sure that file isn't in the standard format exported by Illumina's software. Usually you expect to see columns with the prefix AVG_Signal. The following is a bit of a hack, but will give you an object to play around with;

library(limma)

idata <- read.ilmn("GSE38376_non-normalized.txt",probeid = "PROBE_ID",expr="SKBR")

The limma user guide has examples of processing Illumina data and doing differential expression with these kinds of objects.