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Question: error reading GSE using getGEO()
0
gravatar for jaleh.amo
4 months ago by
jaleh.amo0
jaleh.amo0 wrote:

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 
ADD COMMENTlink modified 4 months ago • written 4 months ago by jaleh.amo0
0
gravatar for James W. MacDonald
4 months ago by
United States
James W. MacDonald48k wrote:

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    
>
ADD COMMENTlink written 4 months ago by James W. MacDonald48k

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!

ADD REPLYlink written 4 months ago by jaleh.amo0
1

Well, your sessionInfo was run prior to loading GEOquery, so nobody can say anything about version problems...

ADD REPLYlink written 4 months ago by James W. MacDonald48k

This is the one after running the library. I also fixed the one I posted originally 

 

> 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 
ADD REPLYlink modified 4 months ago • written 4 months ago by jaleh.amo0
1

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

source("https://bioconductor.org/biocLite.R")
biocLite()
ADD REPLYlink written 4 months ago by James W. MacDonald48k

Someone suggested I use this upgrade and after that it worked.

 

biocLite("BiocUpgrade")
ADD REPLYlink written 4 months ago by jaleh.amo0
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