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.