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 '
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76896/matrix/GSE76896_
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 = col_dou
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
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)
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 usi
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): 1
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
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