Entering edit mode
18 months ago
Nemo • 0
Hello, I have a dataset from GEO, with ID = GSE20206. I have already checked the dataset using the below code in R:
geo.sample <- getGEO("GSE20206", GSEMatrix = TRUE) data1 <- geo.sample[] data2 <- geo.sample[] data3 <- geo.sample[] sample_info <- pData(data1) snp_info <- fData(data2) genotype_info <- exprs(data3)
as I see in sample in this link, which is one of the samples in this dataset, there should be genotype calls for each snp as well. But, when I run the code above, I only get the log-ratio number for each snp not the genotype calls. Could you guide me in this regard?
Even though I am not familiar with getGEO, try accessing the samples individually, e.g. getGEO("GSM517307",...).