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
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and provide commented, minimal, self-contained, reproducible code.
