Where is genotype calls in this dataset?
0
0
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[[1]]
data2 <- geo.sample[[2]]
data3 <- geo.sample[[3]]
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?

genotype snps • 417 views
0
Entering edit mode

Even though I am not familiar with getGEO, try accessing the samples individually, e.g. getGEO("GSM517307",...).