getGEO error
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Entering edit mode
maedakus ▴ 10
@maedakus-9484
Last seen 5.0 years ago

Hi, all

i am a so new to R bioconductor,

now i am trying to download the data of GSE22216 from NCBI GEO data base.

so i write the following script in R.

gset2<-getGEO("GSE22216")

however , unfortunately the error message comes out, and i cannot solve this .

Error in function (type, msg, asError = TRUE)  :
Failed to connect to ftp.ncbi.nlm.nih.gov port 21: Timed out

would you telling me how to solve this ?

takeda in japan

getgeo geoquery • 1.3k views
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Entering edit mode
@gordon-smyth
Last seen 2 hours ago
WEHI, Melbourne, Australia

The error message seems fairly self explanatory: your ftp connection isn't working. To test it, try typing this into your browser address window:

ftp://ftp.ncbi.nlm.nih.gov
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Entering edit mode

hi,

thanks for a good comment, i almost solved this issue, next i am trying to download data using Biolinks package from TCGA database.

in such a case, which ftp connection is necessary to set up, i will open a hole in a fire wall . so i need to specify that FTP connection.