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seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
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Path to urls doesn't work #95

Closed blancahimes closed 5 years ago

blancahimes commented 5 years ago

Several of us tried using GEOquery today, as we have successfully in the past, but it seems like the links to GEO changed so now the queries do not find the proper files. For example,

getGEOSuppFiles("GSE8823") No supplemental files found. Check URL manually if in doubt https://ftp.ncbi.nlm.nih.gov/geo/series/GSE8nnn/GSE8823/suppl/ NULL

I checked the link, and indeed, it is missing. The raw files can still be found at https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE27973&format=file

sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] GEOquery_2.50.5 Biobase_2.42.0 BiocGenerics_0.28.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.3 tidyr_1.0.0 zeallot_0.1.0 crayon_1.3.4 dplyr_0.8.3 assertthat_0.2.1 [7] R6_2.4.0 lifecycle_0.1.0 backports_1.1.5 magrittr_1.5 pillar_1.4.2 rlang_0.4.1
[13] curl_4.2 rstudioapi_0.10 limma_3.38.3 xml2_1.2.2 vctrs_0.2.0 tools_3.5.2
[19] readr_1.3.1 glue_1.3.1 purrr_0.3.3 hms_0.5.2 compiler_3.5.2 pkgconfig_2.0.3 [25] tidyselect_0.2.5 tibble_2.1.3

seandavi commented 5 years ago

NCBI has a habit of updating their ftp site "in place," leading to intermittent failures with finding files. It looks like the situation has resolved, at least for me. 

getGEOSuppFiles("GSE8823")
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE8nnn/GSE8823/suppl//GSE8823_RAW.tar?tool=geoquery'
Content type 'application/x-tar' length 542300160 bytes (517.2 MB)

Could you reopen this if things haven't resolved for you?

Thanks for the report.

blancahimes commented 5 years ago

Thanks for the quick response! All is well now, and I will keep in mind for the future that NCBI links may be down for short periods of time. Funny that these things happen as several students try a command in real time that fails unexpectedly during a class.

seandavi commented 5 years ago

I've had that happen, also. The fallback is to use one of the GEO records packaged with GEOquery or to store the file of interest (often the series matrix file) in a separate location that students can download; GEOquery can parse the file directly.

blancahimes commented 5 years ago

Thanks again!