This package contains functions to read GSE raw data and returns a tidy format. It’s especially useful for chip annotation file, the format of which is really in a messy. You just need to provide the raw data file and it will give you a nice table containing probes and HUGO gene symbols.


if (!('devtools' %in% .packages(T))) install.packages('devtools');


Inpatient people please refer to vignette('rGEO').

For why this package, read this vignette('probe2symbol').


Wired as it seems, it’s best way I can think about so far to maintain reproducibility.

Basically, you make change in R/platform.R, Load All (C-S-L, or ), then Knit R-raw/platform.Rmd to check whether the rule returns exactly what you want. (you can also execute all chunk before, and then repeat modify rule - load- run a specific chunk to save time)