I’m not sure how familiar folks are with the Bioconductor ">Biobase" datasets but one of the free datasets is called ALL (Acute lymphoblastic leukemia). My goal is to calculate and visualize some basic properties of gene expression levels from the ALL dataset. I’m getting stuck on how to write a line of code that's specifically for patients, and another just for genes. I understand that rows=genes and columns=patients, but I do not have the syntax down to specify patients and genes. For example, I have tried:
> median(exprs(ALL))  5.469092
I’m not happy with the results and I know I’m doing something wrong, for example…
…will not calculate the average gene expression levels for each gene. and…
…will not find the average gene expression per gene. Any guidance is super appreciated!