could not find function "getGEO"

Question: could not find function "getGEO"

12 weeks ago by

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

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modified 12 weeks ago by ATpoint ♦ 32k • written 12 weeks ago by Raheleroudi • 0

require(GEOquery) then try again. If not installed, do:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GEOquery")

If Bioconductor is not installed see https://bioconductor.org/install/ and please google for a background in R package management first.

ADD REPLY • link written 12 weeks ago by ATpoint ♦ 32k

Thank you for your response. I have got another error:

> gset <- getGEO("GSE20853", GSEMatrix =TRUE, destdir = "~/proj/lung/data/FUDAN_Expression", AnnotGPL=TRUE)[[1]]
Found 1 file(s)
GSE20853_series_matrix.txt.gz
Error: '~/proj/lung/data/FUDAN_Expression/GSE20853_series_matrix.txt.gz' does not exist.
In addition: Warning messages:
1: In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  :
  URL https://ftp.ncbi.nlm.nih.gov/geo/series/GSE20nnn/GSE20853/matrix/GSE20853_series_matrix.txt.gz: cannot open destfile '~/proj/lung/data/FUDAN_Expression/GSE20853_series_matrix.txt.gz', reason 'No such file or directory'
2: In download.file(sprintf("https://ftp.ncbi.nlm.nih.gov/geo/series/%s/%s/matrix/%s",  :
  download had nonzero exit status

ADD REPLY • link modified 12 weeks ago by zx8754 ♦ 9.1k • written 12 weeks ago by Raheleroudi • 0

Error is pretty clear, check if you have the files:

Error: '~/proj/lung/data/FUDAN_Expression/GSE20853_series_matrix.txt.gz' does not exist.

ADD REPLY • link written 12 weeks ago by zx8754 ♦ 9.1k

I am beginner in this field. Please guide me if I should download the supplementary file from GEO page?

ADD REPLY • link written 12 weeks ago by Raheleroudi • 0

Raheleroudi : You can find the series matrix file on this page at NCBI GEO.

ADD REPLY • link written 12 weeks ago by genomax ♦ 80k

Check that the destdir exists (and create it if not) before calling getGEO

ADD REPLY • link written 12 weeks ago by russhh ♦ 5.2k

One of many reasons listed in below post.

Error: could not find function … in R

ADD REPLY • link written 12 weeks ago by zx8754 ♦ 9.1k

any other suggestions?

ADD REPLY • link written 12 weeks ago by Raheleroudi • 0

The path ~/proj/lung/data/ already exit.

ADD REPLY • link written 12 weeks ago by Raheleroudi • 0

(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.

ADD REPLY • link written 12 weeks ago by russhh ♦ 5.2k

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