Question: could not find function "getGEO"
0
gravatar for Raheleroudi
13 months ago by
Raheleroudi0 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

R • 1.0k views
ADD COMMENTlink modified 13 months ago by ATpoint46k • written 13 months ago by Raheleroudi0

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 REPLYlink written 13 months ago by ATpoint46k

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 REPLYlink modified 13 months ago by zx87549.9k • written 13 months ago by Raheleroudi0

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 REPLYlink written 13 months ago by zx87549.9k

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

ADD REPLYlink written 13 months ago by Raheleroudi0

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

ADD REPLYlink written 13 months ago by GenoMax96k

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

ADD REPLYlink written 13 months ago by russhh5.5k

One of many reasons listed in below post.

ADD REPLYlink written 13 months ago by zx87549.9k

any other suggestions?

ADD REPLYlink written 13 months ago by Raheleroudi0

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

ADD REPLYlink written 13 months ago by Raheleroudi0

(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 REPLYlink written 13 months ago by russhh5.5k
0
gravatar for ATpoint
13 months ago by
ATpoint46k
ATpoint46k wrote:

The directory that you entered does not seem to exist. The command will not auto-create non-existing directories. You have to do it manually, be it with mkdir via command line, dir.create() from inside R or interactively per mouse.

ADD COMMENTlink written 13 months ago by ATpoint46k
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