Question: Downloading Geo Dataset'S Sample Information, But Not Platform Information
2
gravatar for Backlin
7.1 years ago by
Backlin20
Backlin20 wrote:

I want to download the sample information of a 450k methylation array dataset (GSE49031). However, when I try to do so with the R code below I automatically also download and parse a 213.4 MB soft file with the platform information, including annotations for the 485577 probes. This takes a long time and I am not interested in doing it. Is there a way to only get the sample information?

gse <- getGEO("GSE49031", destdir="data")

I tried to be clever and downloaded the series information manually prior to parsing (which is only 24.8 kB), but getGEO still went online and downloaded the platform information.

in.file <- "data/GSE49031_series_matrix.txt.gz"
download.file("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE49nnn/GSE49031/matrix/GSE49031_series_matrix.txt.gz", in.file)
gse <- getGEO(filename=in.file, destdir="data")

I have read the manual and searched for a solution online, but cannot figure out how to do it.

geo R • 3.6k views
ADD COMMENTlink modified 6.3 years ago by Biostar ♦♦ 20 • written 7.1 years ago by Backlin20
1

You might want to look at the GEOmetadb package.

ADD REPLYlink written 7.1 years ago by Sean Davis26k

Thanks for the tip, I'll look into it!

ADD REPLYlink written 7.0 years ago by Backlin20

Interesting question: can you post the solution you might have ...

ADD REPLYlink written 6.8 years ago by Rm8.0k
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