I've downloaded this GSE43013 dataset using GEOquery in R. My understanding is that it contains expression data from liver, kidney, and brain for multiple species. I would like to produce gene expression tables for each species and tissue type. The goal would then be to perform PCA and regression analyses to see if there is a relationship between expression of certain genes and e.g. taxonomic position, diet, etc.
However, I have never worked with gene expression data before so I have very little understanding of the GSE file. I have failed to extract any kind of expression data from the file. Solutions that I have found online do not seem to be working for this dataset (for example producing empty tables where I assume there would normally be data on expression levels). Because of my inexperience I cannot determine why they are not working in this situation.
I would appreciate some help in understanding the format of this file, but most importantly, in figuring out how to pull expression data from it, if that is possible.
EDIT: I still haven't managed to pull data from the GSE file, but looking through the samples associated with the data set (such as this one), I can see that there are files formatted like this:
I assume that the values in the left column refer to specific genes. Perhaps the values in the right column represent expression intensity? If so, would these values be normalized and comparable between species as they are?