I know this question has already been asked in the past, but I found no answer which is suitable for me or is updated to now.
I downloaded a dataset from GEO and I would like to retrieve the genes associated to this dataset, through R and Bioconductor. From what I understood, the gene list is not within the dataset information, and I have to add a step where I download a set ("pd.hugene.1.0.st.v1") containing the associations between Affymetrix probe ID's and genes.
If that's correct, how do I do it?
I thought it was going to be a simple operation, but I don't know how to handle it.
Here's my R script:
options(stringsAsFactors = FALSE) library(oligo) library(GEOquery) source("https://bioconductor.org/biocLite.R") biocLite("affyio") library("affyio") getGEOSuppFiles("GSE59867") list.files("GSE59867") untar("GSE59867/GSE59867_RAW.tar", exdir = "GSE59867/CEL") list.files("GSE59867/CEL") celfiles <- list.files("GSE59867", full = TRUE) rawData <- read.celfiles(celfiles) biocLite("pd.hugene.1.0.st.v1")
How can then get the genes corresponding to the probe sets?