Sofia's Edits

[SI18]

Install additional packages - install.packages("knitr"), install.packages("devtools"), BiocManager::install("limma"), BiocManager::install("GEOquery"), BiocManager::install("ComplexHeatmap"),
The rest of the code runs.
Based on this code, it is hard to understand what is the result and what the original question was. I also do not clearly understand the logic behind arranging the code in this order.

[PAMatusiak]

Sofia, I see that you found a vital error in Tim's code. I found the same error, and to fix it, I used the same code you did. Go team!

My only recommendation is that you insert your BiocManager:: lines of code (lines 22-23) at the beginning, in the first chunk, before load.all (line 19). I get why you put it where you did, but if load.all wont work until you use BiocManager, you might as well put BiocManager first, right?

[Goralsth]

I agree with Paige on this. Everything else looks good

[richard-cassidy]

Good catch on the package installations! I agree that the original code could have been annotated a bit more clearly (especially in the last chunk). Good work!