I already posted a similar issue on bioconductor. https://support.bioconductor.org/p/112607/#112634 Couldn't find a solution.
On Fri, Sep 7, 2018 at 3:45 PM Martin Morgan <mtmorgan.b...@gmail.com> wrote: > Ask on the Bioconductor support site https://support.bioconductor.org > > Provide (on the support site) the output of the R commands > > library(GEOquery) > sessionInfo() > > Also include (copy and paste) the output of the command that fails. I have > > > gseEset2 <- getGEO('GSE76896')[[1]] > Found 1 file(s) > GSE76896_series_matrix.txt.gz > trying URL > ' > https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76896/matrix/GSE76896_series_matrix.txt.gz > ' > Content type 'application/x-gzip' length 40561936 bytes (38.7 MB) > ================================================== > downloaded 38.7 MB > > Parsed with column specification: > cols( > .default = col_double(), > ID_REF = col_character() > ) > See spec(...) for full column specifications. > |=================================================================| 100% > 84 MB > File stored at: > /tmp/Rtmpe4NWji/GPL570.soft > |=================================================================| 100% > 75 MB > > sessionInfo() > R version 3.5.1 Patched (2018-08-22 r75177) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 16.04.5 LTS > > Matrix products: default > BLAS: /home/mtmorgan/bin/R-3-5-branch/lib/libRblas.so > LAPACK: /home/mtmorgan/bin/R-3-5-branch/lib/libRlapack.so > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] 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 > [8] base > > other attached packages: > [1] bindrcpp_0.2.2 GEOquery_2.49.1 Biobase_2.41.2 > [4] BiocGenerics_0.27.1 BiocManager_1.30.2 > > loaded via a namespace (and not attached): > [1] Rcpp_0.12.18 tidyr_0.8.1 crayon_1.3.4 dplyr_0.7.6 > [5] assertthat_0.2.0 R6_2.2.2 magrittr_1.5 pillar_1.3.0 > [9] stringi_1.2.4 rlang_0.2.2 curl_3.2 limma_3.37.4 > [13] xml2_1.2.0 tools_3.5.1 readr_1.1.1 glue_1.3.0 > [17] purrr_0.2.5 hms_0.4.2 compiler_3.5.1 pkgconfig_2.0.2 > [21] tidyselect_0.2.4 bindr_0.1.1 tibble_1.4.2 > > On 09/07/2018 06:08 AM, Deepa wrote: > > Hello, > > > > I am using a bioconductor package in R. > > The command that I use reads the contents of a file downloaded from a > > database and creates an expression object. > > > > The syntax works perfectly fine when the input size is of 10 MB. Whereas, > > when the file size is around 40MB the object isn't created. > > > > Is there an efficient way of loading a large input file to create the > > expression object? > > > > This is my code, > > > > > > library(gcrma) > > library(limma) > > library(biomaRt) > > library(GEOquery) > > library(Biobase) > > require(GEOquery) > > require(Biobase) > > gseEset1 <- getGEO('GSE53454')[[1]] #filesize 10MB > > gseEset2 <- getGEO('GSE76896')[[1]] #file size 40MB > > > > ##gseEset2 doesn't load and isn't created > > > > Many thanks > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
