Hi, I am quite new to R and I have been trying to use a dataset from the GEO database (GEO104438) that is interesting to my PhD work. The file that I have been able to download and use in R, is a table with ID references and then the normalised signal intensity values for all of the donors (and cell types). I have put a screenshot of the table for reference.
I am hoping to try look at whether there are any genes that are differentially expressed depending on what cell type they are (as they are both derived from a common precursor). So for each donor I have 2 different cell types. Due to this, I was initially trying to tell R that my data is paired but I am stuck.
I have been reading online and trying to use the limma guide but I am completely confused as all of the examples I have seen online are not in a similar format to this dataset.
I would appreciate any help!