Importing GEO dataset

Question

[gina02]

I need to import data GSE76124 in R studio the command I used is library(GEOquery) my_id <- "GSE76124" gse <- getGEO(my_id)

the output and warning I'm getting is : Found 1 file(s) GSE76124_series_matrix.txt.gz trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76124/matrix/GSE76124_series_matrix.txt.gz'

Content type 'application/x-gzip' length 58695125 bytes (56.0 MB)

downloaded 56.0 MB

Error: The size of the connection buffer (131072) was not large enough
to fit a complete line:

• Increase it by setting Sys.setenv("VROOM_CONNECTION_SIZE")

how do I fix it?

Answer 1

[Basti]

Increasing the default buffer size will solve your issue :

library(GEOquery) 
Sys.setenv("VROOM_CONNECTION_SIZE"=131072*100)
my_id <- "GSE76124" 
gse <- getGEO(my_id)

If it still doesn't work, you can try to increase the size.

Answer 2

[Sean Davis]

It looks like you might be using an outdated version of GEOquery. Upgrading will likely fix the issue.

The problem arises here because of the behavior of the readr package changing. GEOquery no longer uses readr; hence the interest in upgrading.

[gina02]

thank you for responding I have updated to the latest version of GEOquery from the official website https://www.bioconductor.org/packages/release/bioc/html/GEOquery.html and i'm still getting the same error

[Sean Davis]

I should have been more specific. To upgrade to the newest GEOquery version, you'll need to be running R 4.1 or later. If you are still having problems after updating R and reinstalling Bioconductor, supply the output of sessionInfo() so we can check what is going on with versions.

As an alternative, see the excellent answer by @bastiducreux.

[gina02]

my sessionInfo() output is R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.2.2

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_4.1.1 tools_4.1.1

[Sean Davis]

What is the output of sessionInfo() after loading GEOquery (with library(GEOquery))? That will tell us the installed GEOquery version. Sorry for the hassle.

[gina02]

no hassle thanks for helping.. the output ii got is

R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.2.2

Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: character(0)

other attached packages: [1] GEOquery_2.60.0

loaded via a namespace (and not attached): [1] xml2_1.3.2 magrittr_2.0.1 BiocGenerics_0.38.0 hms_1.1.1
[5] grDevices_4.1.1 tidyselect_1.1.1 R6_2.5.1 rlang_0.4.12
[9] fansi_0.5.0 dplyr_1.0.7 tools_4.1.1 utils_4.1.1
[13] parallel_4.1.1 Biobase_2.52.0 utf8_1.2.2 DBI_1.1.1
[17] stats_4.1.1 ellipsis_0.3.2 datasets_4.1.1 assertthat_0.2.1
[21] tibble_3.1.6 base_4.1.1 lifecycle_1.0.1 crayon_1.4.2
[25] purrr_0.3.4 readr_2.1.0 tzdb_0.2.0 tidyr_1.1.4
[29] graphics_4.1.1 vctrs_0.3.8 glue_1.5.0 limma_3.48.3
[33] compiler_4.1.1 pillar_1.6.4 methods_4.1.1 generics_0.1.1
[37] pkgconfig_2.0.3

[Sean Davis]

This output is really helpful. It looks like you are using Bioconductor version 3.13. We need to get up updated to 3.14. To do so:

BiocManager::install(version="3.14")

You'll be asked if you want to update packages (and it may be a large number) to which you can answer "Yes". This will upgrade not just GEOquery but all Bioconductor packages to the new Bioconductor version. After doing so, when you redo the sessionInfo() in a new R session, you'll see that GEOquery version is 2.62.1 (or later).