getGEO is taking too long time for a file that is already locally cached
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alptaciroglu ▴ 50
@alptaciroglu-8859
Last seen 4.6 years ago
Turkey

I am using getGEO() function from GEOquery package to retrieve a dataset that I previously downloaded. It says using locally cached version of series matrix file and again locally cached version of GPL570 file. If I download series matrix file from GEO and read it by read.table it takes couple of seconds but using getGEO function it takes 2-3 mins. I would appreciate if you could let me know if there is a way to fasten the process or maybe explain what is going on. Thanks and here is my session info.

 

R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GEOmetadb_1.28.0      RSQLite_1.0.0         DBI_0.3.1             RCurl_1.95-4.7        bitops_1.0-6         
 [6] XML_3.98-1.3          rvest_0.3.1           xml2_0.1.2            xlsx_0.5.7            xlsxjars_0.6.1       
[11] rJava_0.9-8           shinyjs_0.4.0         hgu133plus2cdf_2.16.0 Hmisc_3.17-0          Formula_1.2-1        
[16] survival_2.38-3       lattice_0.20-33       ggplot2_1.0.1         seqinr_3.1-3          ade4_1.7-3           
[21] DT_0.1                xtable_1.8-2          som_0.3-5             GEOquery_2.34.0       affy_1.46.1          
[26] Biobase_2.28.0        BiocGenerics_0.14.0   shiny_0.12.2          BiocInstaller_1.18.5 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.3           digest_0.6.9          mime_0.4              R6_2.1.2              GenomeInfoDb_1.4.3   
 [6] plyr_1.8.3            acepack_1.3-3.3       stats4_3.2.2          httr_1.1.0            zlibbioc_1.14.0      
[11] S4Vectors_0.6.6       rpart_4.1-10          preprocessCore_1.30.0 proto_0.3-10          labeling_0.3         
[16] splines_3.2.2         stringr_1.0.0         selectr_0.2-3         foreign_0.8-65        htmlwidgets_0.5      
[21] munsell_0.4.2         httpuv_1.3.3          htmltools_0.3         nnet_7.3-10           gridExtra_2.0.0      
[26] IRanges_2.2.9         MASS_7.3-43           jsonlite_0.9.19       gtable_0.1.2          magrittr_1.5         
[31] scales_0.3.0          stringi_1.0-1         reshape2_1.4.1        affyio_1.36.0         latticeExtra_0.6-26  
[36] RColorBrewer_1.1-2    tools_3.2.2           yaml_2.1.13           AnnotationDbi_1.30.1  colorspace_1.2-6     
[41] cluster_2.0.3  

getgeo r • 1.1k views
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