Entering edit mode
3.6 years ago
michael.s
▴
10
I have previously downloaded all the raw files from GEO in the wd. Then, I run the following code:
> library(crossmeta)
> # specify where data will be downloaded
> data_dir <- file.path(getwd())
> # gather all GSEs
> gse_names <- c("GSE88", "GSE89", "GSE3167")
> get_raw(gse_names, data_dir)
> esets <- load_raw(gse_names, data_dir)
After get_raw
, the .cel files are successfully extracted from .tar raw files. But, after load_raw
I get the following error message:
https://ftp.ncbi.nlm.nih.gov/geo/series/GSEnnn/GSE88/matrix/
Error in function (type, msg, asError = TRUE) :
error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘annotation’ for signature ‘"character"’
My session info are:
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
crossmeta_1.16.1 GEOquery_2.58.0 Biobase_2.50.0
Cross-posted: https://support.bioconductor.org/p/p134806/#p134806