Question

getGEO error

0

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maedakus ▴ 10

@maedakus-9484

Last seen 8.2 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 ?

thanks in advance.

takeda in japan

getgeo geoquery • 2.0k views

ADD COMMENT • link updated 8.9 years ago by Gordon Smyth 51k • written 8.9 years ago by maedakus ▴ 10

score 2 · Answer 1 · 2016-01-08

2

Entering edit mode

Gordon Smyth 51k

@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

ADD COMMENT • link 8.9 years ago • updated 8.8 years ago Gordon Smyth 51k

0

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.

thanks in advance.

ADD REPLY • link 8.8 years ago maedakus ▴ 10