error reading GSE using getGEO()
1
@jalehamo-16527
Last seen 6.4 years ago
I am trying to read a GSE file and getting this following error.
gg = getGEO("GSE6929", GSEMatrix = TRUE)
but I receive the following error
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE6nnn/GSE6929/matrix/
OK
Found 2 file(s)
/geo/series/GSE6nnn/GSE6929/
Error in file(con, "r") : cannot open the connection
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/GSE6nnn/GSE6929/matrix//geo/series/GSE6nnn/GSE6929/: cannot open destfile '/tmp/RtmpFquqz8//geo/series/GSE6nnn/GSE6929/', 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
3: In file(con, "r") :
cannot open file '/tmp/RtmpFquqz8//geo/series/GSE6nnn/GSE6929/': No such file or directory
I am not sure if the issue is with the package or the version of R I am using. This is my sessionifo()
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GEOquery_2.42.0 Biobase_2.36.2 BiocGenerics_0.22.1
loaded via a namespace (and not attached):
[1] httr_1.3.1 compiler_3.5.0 R6_2.2.2 tools_3.5.0 RCurl_1.95-4.11 bitops_1.0-6 XML_3.98-1.12
r
geo
getgeo
• 1.8k views
@james-w-macdonald-5106
Last seen 3 days ago
United States
Sometimes queries over the internet don't work, and you have to try again.
> gg = getGEO("GSE6929", GSEMatrix = TRUE)
Found 1 file(s)
GSE6929_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE6nnn/GSE6929/matrix/GSE6929_series_matrix.txt.gz'
Content type 'application/x-gzip' length 2099151 bytes (2.0 MB)
downloaded 2.0 MB
Parsed with column specification:
cols(
ID_REF = col_character(),
GSM159830 = col_double(),
GSM159831 = col_double(),
GSM159832 = col_double(),
GSM159833 = col_double(),
GSM159834 = col_double(),
GSM159835 = col_double(),
GSM159837 = col_double(),
GSM159838 = col_double()
)
File stored at:
C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpSeDyse/GPL1355.soft
|=================================================================| 100% 40 MB
> gg[[1]]
ExpressionSet (storageMode: lockedEnvironment)
assayData: 31099 features, 8 samples
element names: exprs
protocolData: none
phenoData
sampleNames: GSM159830 GSM159831 ... GSM159838 (8 total)
varLabels: title geo_accession ... Strain:ch1 (33 total)
varMetadata: labelDescription
featureData
featureNames: 1367452_at 1367453_at ... AFFX_ratb2/X14115_at (31099
total)
fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total)
fvarMetadata: Column Description labelDescription
experimentData: use 'experimentData(object)'
Annotation: GPL1355
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] bindrcpp_0.2.2 GEOquery_2.48.0 Biobase_2.40.0
[4] BiocGenerics_0.26.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 tidyr_0.8.1 dplyr_0.7.6 assertthat_0.2.0
[5] R6_2.2.2 magrittr_1.5 pillar_1.2.3 stringi_1.1.7
[9] rlang_0.2.1 curl_3.2 limma_3.36.2 xml2_1.2.0
[13] tools_3.5.0 readr_1.1.1 glue_1.2.0 purrr_0.2.5
[17] hms_0.4.2 compiler_3.5.0 pkgconfig_2.0.1 tidyselect_0.2.4
[21] bindr_0.1.1 tibble_1.4.2
>
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I have been trying for the past 2 days. That's why I am not sure if the issue is our version of R at work or something else! I see getGEO() works for others!
Well, your
sessionInfo
was run prior to loadingGEOquery
, so nobody can say anything about version problems...This is the one after running the library. I also fixed the one I posted originally
You have borked your Bioc installation. You should not have any of those package versions for R-3.5.0. You need to restart R, and then do
Someone suggested I use this upgrade and after that it worked.