Question: could not find function "getGEO"
0
gravatar for Raheleroudi
12 weeks 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 • 191 views
ADD COMMENTlink modified 12 weeks ago by ATpoint32k • written 12 weeks 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 12 weeks ago by ATpoint32k

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 12 weeks ago by zx87549.1k • written 12 weeks 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 12 weeks ago by zx87549.1k

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

ADD REPLYlink written 12 weeks ago by Raheleroudi0

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

ADD REPLYlink written 12 weeks ago by genomax80k

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

ADD REPLYlink written 12 weeks ago by russhh5.2k

One of many reasons listed in below post.

ADD REPLYlink written 12 weeks ago by zx87549.1k

any other suggestions?

ADD REPLYlink written 12 weeks ago by Raheleroudi0

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

ADD REPLYlink written 12 weeks 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 12 weeks ago by russhh5.2k
0
gravatar for ATpoint
12 weeks ago by
ATpoint32k
Germany
ATpoint32k 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 12 weeks ago by ATpoint32k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1216 users visited in the last hour