Re: [R] Efficient way of loading files in R

Martin, I forgot to mention. The same command works fine when I try,gseEset2 <- getGEO('GSE76896') , without saving the file to a destination folder . Output: Found 1 file(s) GSE76896_series_matrix.txt.gz trying URL '

Re: [R] Efficient way of loading files in R

I am also providing the output that I obtain for your kind reference, gseEset2 <- getGEO('GSE76896', destdir = "data/")[[1]] Found 1 file(s) GSE76896_series_matrix.txt.gz Using locally cached version: /data//GSE76896_series_matrix.txt.gz Parsed with column specification: cols( .default =

Re: [R] Efficient way of loading files in R

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 wrote: > Ask on the Bioconductor support site https://support.bioconductor.org > > Provide (on the support site) the output

Re: [R] Efficient way of loading files in R

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)

Re: [R] Efficient way of loading files in R

getgeo() seems to be a custom routine. Import the file in reader and confirm that's a CSV file from Excel. If this is a non standard input, custom subroutine is creating new constraints. Usually R has no problem till workspace is 1 gb On Fri 7 Sep, 2018, 15:38 Deepa, wrote: > Hello, > > I am

Re: [R] Efficient way of loading files in R

The following is the system configuration: Architecture: x86_64 CPU op-mode(s):32-bit, 64-bit Byte Order:Little Endian CPU(s):4 On-line CPU(s) list: 0-3 Thread(s) per core:2 Core(s) per socket:2 Socket(s): 1 NUMA node(s):

[R] Efficient way of loading files in R

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.