Question: How to map Affymetrix probe ID's from a GEO dataset to corresponding gene symbols?
1
gravatar for Davide Chicco
5 months ago by
Canada
Davide Chicco80 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 • 370 views
ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 5 months ago by Davide Chicco80

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

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax65k
1
gravatar for Kevin Blighe
5 months ago by
Kevin Blighe41k
Guy's Hospital, London
Kevin Blighe41k 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 5 months ago by Kevin Blighe41k
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