Question: How to map Affymetrix probe ID's from a GEO dataset to corresponding gene symbols?
1
gravatar for Davide Chicco
2.3 years ago by
Davide Chicco110
Canada
Davide Chicco110 wrote:

Hi

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?

Thanks

-- Davide

bioconductor R geo • 1.1k views
ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 2.3 years ago by Davide Chicco110

You could use Download full table link on this page (scroll down) to get linked annotation table for this platform.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by GenoMax96k
1
gravatar for Kevin Blighe
2.3 years ago by
Kevin Blighe70k
Republic of Ireland
Kevin Blighe70k wrote:

You can do this automatically. Just take a look here: A: Affymetrix Human Genome U133 Plus 2.0 Array

The only difference that you need to do is to use affy_hugene_1_0_st_v1 where I have used affy_hg_u133_plus_2

ADD COMMENTlink written 2.3 years ago by Kevin Blighe70k
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