Question: Access metadata in GEO expression datasets
0
gravatar for priya.bmg
7 days ago by
priya.bmg0
priya.bmg0 wrote:

Hi,

I have been trying to analyze expression datasets from NCBI GEO database. Because of memory allocation problem, I am not able to load the expression text file in R. But I could save the SOFT file in temporary file location. Is there a way to access few rows and columns in this SOFT file? I tried using GEOquery R package and I can't access the meta data

Thanks

Priya

gene expression R geo • 78 views
ADD COMMENTlink modified 6 days ago • written 7 days ago by priya.bmg0

Can you post the code that you have tried to access the file?

ADD REPLYlink written 6 days ago by svp240
gds <- getGEO("GSE25219")

Got the below error message:

Found 2 file(s)

GSE25219-GPL5175_series_matrix.txt.gz

Using locally cached version: C:\Users\dell\AppData\Local\Temp\RtmpGGb51t/GSE25219-GPL5175_series_matrix.txt.gz

Error in read_lines_(ds, skip_empty_rows = skip_empty_rows, locale_ = locale,  : 

Cannot read file C:/Users/dell/AppData/Local/Temp/RtmpGGb51t/file130c7d4d52f1: Not enough storage is available to process this command.
ADD REPLYlink modified 6 days ago by genomax91k • written 6 days ago by priya.bmg0

The error message is telling you don't have enough device space.

ADD REPLYlink written 6 days ago by MatthewP780

Yes there is not enough memory to load the data using the getGEO command. Is there a way around to save the data and do the analysis without much memory usage?

ADD REPLYlink written 6 days ago by priya.bmg0
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