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