Accessing gene names from an Affymetrix GeneFeatureSet
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8 weeks ago
Bryan • 0

I'm attempting to create a gene to expression matrix based upon the data from GSE39420. When I download and unzip the raw data (a bunch of .CEL files), I load them into R using oligo and get below, including all the expression level data. However, there are no gene names as far as I can tell (nothing in the featureData as seen below). I'm newer to Affymetrix data processing - are he gene names someplace I'm missing? Thanks!

The test object containing

R Affymetrix Microarray GEO • 312 views
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8 weeks ago
GenoMax 121k

You can find the gene names in the platform files (that contain annotation) for this chip: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL11532

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Thanks - but my issue is I can't seem to find any information about the actual probes used in this dataset. Essentially I just have expression data and no rownames (ie featureNames). Not sure if this is buried somewhere in the GeneFeatureSet object itself that I'm missing or I'm meant to pull it somewhere else. For reference, this is how I pulled the dataset into R:

BiocManager::install("oligo")
library(oligo)
test_list <- list.files("/Volumes/GoogleDrive/My\ Drive/Bangelo_Lab/AD_Resilience_Project/Brain_Seq_MetaAnalysis/Datasets/Bulk/GSE39420/extracted/", full.names=TRUE)
test <- read.celfiles(test_list)
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