How can I upload GEO files (.soft.gz) in R?

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Pranavathiyani G

You can try with GEOquery, a Bioconductor package.

https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.R

https://bioconductor.org/packages/release/bioc/html/GEOquery.html

Mahmoud Ahmed

By upload, I assume you mean load the .soft.gz in R session. This depends on whether you have the file on your local machine or you will download it using GEO accession number. Either ways, function getGEO will do as @Otoniel just explained. Once you have the file on your local machine and loaded in the R session as object data, you can use the operator '$' to get the desired object from the file.

Greeshma Thulasi

We can use the Import Dataset option from the File menu and can upload our dataset(whether in CSV, Excel, SPSS, SAS or Statistical data ) to the GEO.