Problem with getGEO

Dear all

I want to extract the expression values of a gene from GSE75970 in my Mac Sierra 10.12.6 with R 3.3.1 and RStudio Version 0.99.903. First I run this code:

library(GEOquery)
gse <- getGEO("GSE75970")

I faced this: enter image description here

Furthermore, I used

    options('download.file.method.GEOquery' = 'curl')

But did not work.

Please help me.

geoquery downlaod gse75970

• 1,841 views • link

written 8.4 years ago by sina.majidian 2

I was able to download the file:

> getGEO("GSE75970")
Found 1 file(s)
GSE75970_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE75nnn/GSE75970/matrix/GSE75970_series_matrix.txt.gz'
Content type 'application/x-gzip' length 1661409 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

Parsed with column specification:
cols(
  ID_REF = col_character(),
  GSM1971104 = col_double(),
  GSM1971105 = col_double(),
  GSM1971106 = col_double(),
  GSM1971107 = col_double(),
  GSM1971108 = col_double(),
  GSM1971109 = col_double(),
  GSM1971110 = col_double(),
  GSM1971111 = col_double()
)
File stored at: 
/var/folders/5r/s597hc5j3w93_x8_tn57w3g80000gn/T//RtmpIzAmi9/GPL14550.soft

Try upgrading to the latest version of Bioconductor using:

source("https://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

Then upgrade all your packages with:

source("https://bioconductor.org/biocLite.R")
biocLite()

• 1 views • link

written 8.4 years ago by James Ashmore 347

Thank you vey much. Your solution works.

• 1 views • link

written 8.4 years ago by sina.majidian 2

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