Question: getGEO from GEOquery doesn't return probesets
0
gravatar for dnedveck
20 months ago by
dnedveck0
USA/Michigan
dnedveck0 wrote:

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 • 388 views
ADD COMMENTlink modified 20 months ago by James W. MacDonald51k • written 20 months ago by dnedveck0
Answer: getGEO from GEOquery doesn't return probesets
2
gravatar for James W. MacDonald
20 months ago by
United States
James W. MacDonald51k wrote:
> 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    
> 
ADD COMMENTlink written 20 months ago by James W. MacDonald51k

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. 

ADD REPLYlink written 19 months ago by dnedveck0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 176 users visited in the last hour