I want to access a GEO dataset and I followed the instructions here: https://sbc.shef.ac.uk/geo_tutorial/tutorial.nb.html
When I want to see the expression data
exprs(gse) I only get the GSMs and there is a logical class output. I then downloaded the
_RAW.rar of the GEO and constructed a phenotype/metadata table with the individual GSMs (.tab.gz.) as rownames. Is there an easy way to create a matrix table from the pheontype/metadata table I've constructed, without the need to manually load the individual GSMs?! In this example this was done with
library(affy) for CEL files: https://www.stat.purdue.edu/bigtap/online/docs/Introduction_to_Microarray_Analysis_GSE15947.html - however this library doesn't apply to my files, which are RNA seq files (.tab.gz.)
Thank you very much!