Question: how to fix error in getGEO function?
0
gravatar for maryam.sabet
2.3 years ago by
maryam.sabet0 wrote:

When I want to use the getGEO function to download GSE dataset with this code:

series <- "GSE85358" gset <- getGEO(series , GSEMatrix =TRUE, AnnotGPL=TRUE, destdir = "....." ) I encounter this error:

https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/ Error in function (type, msg, asError = TRUE) : error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version

How can i fix it?

R software error • 1.5k views
ADD COMMENTlink written 2.3 years ago by maryam.sabet0

What is the output of sessonInfo()?

ADD REPLYlink written 2.3 years ago by h.mon31k

Hello Mr. h.mon, sorry for that but I noticed that you're from Brazil. And I would like to know about your projects here, could you please send me an email? I can't see your email on your account on biostars :/

Best regards!

ADD REPLYlink modified 2.3 years ago by h.mon31k • written 2.3 years ago by geocarvalho150

Hello geocarvalho , I deleted your contact information from the post - if you really want it public, it is probably better to add it to your profile page.

I don't have projects, I am a mix of (IT / analysis / emotional) support staff - being reasonably good at the first two, while sucking big time at the third.

ADD REPLYlink written 2.3 years ago by h.mon31k

h.mon LOL, I still thinking that you're a Jedi here! Any chance we can talk by email or chat?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by geocarvalho150

It seems that you have not the right setup for the https: downloads. Are you on windows or Linux?

Can you dload a file over https:// in R? For example, does the following command work inside your R?

download.file("https://ftp.ncbi.nlm.nih.gov/geo/series/GSE2nnn/GSE2553/matrix/GSE2553_series_matrix.txt.gz", destfile="tmp")
ADD REPLYlink written 2.3 years ago by Santosh Anand5.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1520 users visited in the last hour