CODEWITHSUNDEEP
r
Fariba
Fariba

Reputation: 19

download GEO data from NCBI to R

I am trying to learn bioinformatic analyses using R & Bioconductor by myself but at early steps I stucked! I was trying to download GSE data from NCBI and follow some commands that I found in youtube but you can see the error messages as following:

# First Step:
library(GEOquery) 
Error in library(GEOquery) : there is no package called ‘GEOquery’

# Second step:
require(GEOquery) 
Loading required package: 
GEOquery Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :   
  there is no package called ‘GEOquery’ 
library(GEOquery) 
Error in library(GEOquery) : there is no package called ‘GEOquery’ 

# Third step:
source("https://bioconductor.org/biocLite.R") 
Error in file(filename, "r", encoding = encoding) :    
  cannot open the connection 
In addition: Warning message: In file(filename, "r", encoding = encoding) : unsupported URL scheme

# Forth step:
biocLite("GEOquery") 
Error: could not find function "biocLite"

Upvotes: 1

Views: 1089

Answers (2)

A. Liberzon
A. Liberzon

Reputation: 11

biocLite() is a function from the Bioconductor package. To use it, you'll need to install Bioconductor first.

Upvotes: 0

lemonC
lemonC

Reputation: 78

It seems like you did not install the package yet. First thing, you should do install.packages("GEOquery").

For your 3rd step, I am not sure if https://bioconductor.org/biocLite.R is an R script published online or what, I tried to open but it says cannot be found. I assume you would like to run an R script here since you used source(). If you have the R script, save it to your directory, so get the directory path and put it in source(), then you can run it successfully.

Then for your fourth step, it was because you did not run the biocLite.R correctly, the function did not save to the environment, that was why it failed and gave you an error.

Overall, two main problems you had: 1. you did not download the package (caused 1st and 2nd steps to fail) 2. argument in source() was wrong, cause 3rd and 4th to fail.

Hope this helps.

Upvotes: 1

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