This is probably a very novice question but I've been spending many days on it. Any pointers would be appreciated!

I was able to read the cell lines of E-MTAB-3610 (link below) into R using the ArrayExpress package. There were around 1,000 columns of cells lines with 553,536 (=774x774) rows of genes.

https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3610/

My next step is to find a row names for the dataset above. In the site above, I took the Array Design file ("A-GEOD-13667.adf.txt"), which contains probe-sets and their gene counterparts. I read it in R, and separate them into multiple rows using the code below.

df <- read_delim("A-GEOD-13667.adf.txt", 
             delim = "\t", escape_double = FALSE, 
             trim_ws = TRUE, skip = 15)
df <- separate_rows(df,`Reporter Database Entry [genbank]`,sep=";")

However, this resulted in 96,223 instead of 553,536 rows. I went through some papers (i.e. below) and saw that they were able to find an association between probe-sets and gene symbols using package hgu219.db.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6406180/

I looked into the package and was not able to replicate 553,536 rows as well. Lastly, I looked into the package hgu219cdf below, which contains an index i from 1 to 553536. Except than that, I was not able to find anything only that would tie back to this row count.

http://bioconductor.org/packages/release/data/annotation/manuals/hgu219cdf/man/hgu219cdf.pdf

Thanks again for your suggestion!