I am trying to access some unpublished data from GEO for which I know the GSE number and the access token. I would like to download it. However, I couldn't download it using getGEO.

I tried both using just the GSE and with a modified version with the token at the end

gse <- getGEO("GSE01010101")
gse <- getGEO("GSE01010101&?token=randomletters")

In both cases the response I get is:

Error in open.connection(x, "rb") : HTTP error 404.

I haven't found anything online or in the help pages of GEOquery, but I might have missed it. Or maybe there is another solution outside GEOquery package

How can I download the data using GEOquery?

Unfortunately, I don't have that functionality implemented. You can download the series matrix files by hand and then read them using getGEO, though.

I will not be able to get to it soon, but if you want, feel free to file an issue to add reviewer link functionality (https://www.ncbi.nlm.nih.gov/geo/info/faq.html#revieweraccess).