I am trying to load gene expression and phenotype data into R from a particular study that can be accessed at the GEO database (id: GSE72680) or at the ArrayExpress database (id: E-GEOD-72680). I have tried using both the GEOquery and ArrayExpress R packages to load this data into R but have been unsuccessful. I am wondering if anyone could help show me how to load the gene expression and phenotype data from this study into R. Thanks!
You'll need to download the supplementary files from GEO and then determine the best approach to process them. You can use the getGEOSuppFiles() function to download those raw data files. The phenoData from a getGEO() call can still be useful, though, for building out the sample information.