getGEO from GEOquery doesn't return probesets
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0
Entering edit mode
dnedveck • 0
@dnedveck-15341
Last seen 3.3 years ago
USA/Michigan

I'm running into an issue with GEOquery not loading in probeset names as rows in a dataset. I'm reproducing an analysis that someone else did, and reading their output, they didn't have any issues loading the same dataset. Any help on why there are no probesets would be much appreciated.

Here's code that can reproduce the error that I am getting:

library(Biobase)
library(GEOquery)

eset <- getGEO("GSE66099")[[1]]
str(eset)

eset.exprs <- exprs(eset)
str(eset.exprs)

When I run the code, this is what I get for str(eset.exprs), note the NA.1, NA.2 row.names

str(eset.exprs)
##  num [1:54675, 1:276] 2.74 4.34 7.11 3.67 1.78 ...
##  - attr(*, "dimnames")=List of 2
##   ..$ : chr [1:54675] "NA" "NA.1" "NA.2" "NA.3" ...
##   ..$ : chr [1:276] "GSM1617492" "GSM1617493" "GSM1617494" "GSM1617495" ...

and here's my sessionInfo()

## R version 3.4.3 (2017-11-30)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 7 x64 (build 7601) Service Pack 1
## 
## 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        GEOquery_2.46.15    Biobase_2.38.0     
## [4] BiocGenerics_0.24.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.15     xml2_1.2.0       knitr_1.20       bindr_0.1       
##  [5] magrittr_1.5     hms_0.4.1        tidyselect_0.2.4 R6_2.2.2        
##  [9] rlang_0.2.0      stringr_1.3.0    dplyr_0.7.4      tools_3.4.3     
## [13] htmltools_0.3.6  yaml_2.1.18      rprojroot_1.3-2  digest_0.6.15   
## [17] assertthat_0.2.0 tibble_1.4.2     purrr_0.2.4      tidyr_0.8.0     
## [21] readr_1.1.1      curl_3.1         glue_1.2.0       evaluate_0.10.1 
## [25] rmarkdown_1.9    limma_3.34.9     stringi_1.1.6    compiler_3.4.3  
## [29] pillar_1.2.1     backports_1.1.2  pkgconfig_2.0.1
geoquery getgeo probeset • 571 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States
> eset <- getGEO("GSE66099")[[1]]
Found 1 file(s)
GSE66099_series_matrix.txt.gz
trying URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66099/matrix/GSE66099_series_matrix.txt.gz'
Content type 'application/x-gzip' length 81901666 bytes (78.1 MB)
downloaded 78.1 MB

Parsed with column specification:
cols(
  .default = col_double(),
  ID_REF = col_character()
)
See spec(...) for full column specifications.
|=================================================================| 100%  171 MB
File stored at:
C:\Users\AAJM-M~1\AppData\Local\Temp\Rtmpu8lvwY/GPL570.soft
> head(featureNames(eset))
[1] "1007_s_at" "1053_at"   "117_at"    "121_at"    "1255_g_at" "1294_at" 
> head(row.names(exprs(eset)))
[1] "1007_s_at" "1053_at"   "117_at"    "121_at"    "1255_g_at" "1294_at" 
> 

> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

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        GEOquery_2.46.15    Biobase_2.38.0     
[4] BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.15     tidyr_0.8.0      dplyr_0.7.4      assertthat_0.2.0
 [5] R6_2.2.2         magrittr_1.5     pillar_1.2.1     stringi_1.1.6   
 [9] rlang_0.2.0      curl_3.1         limma_3.34.9     xml2_1.2.0      
[13] tools_3.4.3      readr_1.1.1      glue_1.2.0       purrr_0.2.4     
[17] hms_0.4.1        compiler_3.4.3   pkgconfig_2.0.1  tidyselect_0.2.4
[21] bindr_0.1        tibble_1.4.2    
> 
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0
Entering edit mode

Thanks for your quick response -- I'm not sure what was happening on my machine, but after a few restarts I'm getting the probenames now. 

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