Importing with GEOquery

Question

[MarjoryMollusc]

I am attempting to learn a bit more about processing RNA-seq data, and I am starting off by trying to recreate some figures from a paper. To do this I need to import the data from GEO. They have stored they data in SubSeries and SuperSeries and I have been attempting to download the SubSeries and use the data. I initially tried importing that data into R using:

mRNA_data <- getGEO('GSE42379', GSEMatrix=TRUE)

When looking at the data, it downloaded into two separate GSE series. I have been unable to access the data from both of those GSE files, as it only seems to parse the first of the files. Is this because the data was obtained on two different platforms? How would I be able to access the data in the second GSE series? The only way I have found that will access all the data is if you use GSEMatrix=FALSE which parses all 28 samples but then to access them is a complete nightmare, which again is not all that well explained (or at least to my limited abilities/understanding). The data I am trying to access is here.

Thanks

Answer 1

[Sean Davis]

GEOquery always returns a list when using GSEMatrix = TRUE for exactly situations like this where the Series record has data from multiple platforms.

library(GEOquery)
mRNA_data <- getGEO('GSE42379', GSEMatrix=TRUE)
names(miRNA_data)
length(miRNA_data)
# mRNA_data is a `list`
human_data = mRNA_data[["GPL8759"]]
mouse_data = mRNA_data[["GPL8321"]]
human_data

Now, human_data and mouse_data are each ExpressionSet objects.

[MarjoryMollusc]

Oh my goodness I feel like an idiot. That's so obvious. So it can also just be done with mRNA_data[[1]] and mRNA_data[[2]]