Question: could not find function "getGEO"
0
Raheleroudi • 0 wrote:
Dear all
I am analyzing gene expression data (GEO) in R (in LINUX). I got the below error in my running;
could not find function "getGEO"
Please guide me in this matter,
Best wishes,
Raheleh
ADD COMMENT
• link
•
modified 13 months ago
by
ATpoint ♦ 46k
•
written
13 months ago by
Raheleroudi • 0
require(GEOquery)
then try again. If not installed, do:If Bioconductor is not installed see https://bioconductor.org/install/ and please google for a background in R package management first.
Thank you for your response. I have got another error:
Error is pretty clear, check if you have the files:
I am beginner in this field. Please guide me if I should download the supplementary file from GEO page?
Raheleroudi : You can find the series matrix file on this page at NCBI GEO.
Check that the destdir exists (and create it if not) before calling getGEO
One of many reasons listed in below post.
any other suggestions?
The path ~/proj/lung/data/ already exit.
(That isn't an answer, it's a reply to a comment). Nonethless, please check if the _destdir_ exists, that is,
~/proj/lung/data/FUDAN_Expression
, not~/proj/lung/data
.