[R] Efficient way of loading files in R

Amit Mittal pro|@@m|t@m|tt@| @end|ng |rom gm@||@com
Fri Sep 7 12:11:58 CEST 2018

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, <deepamahm.iisc using gmail.com> 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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Amit Mittal
Pursuing Ph.D. in Finance and Accounting
Indian Institute of Management, Lucknow
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