Help with accessing GEO dataset
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Entering edit mode
9 weeks ago
Sharon ▴ 10

Hi. I am trying to access a GEO dataset by following the instructions in a tutorial. However, I am unable to. I keep on getting this message.

Found 1 file(s)
GSE33126_series_matrix.txt.gz
Using locally cached version: C:\Users\Sharon\AppData\Local\Temp\RtmpmaCHbX/GSE33126_series_matrix.txt.gz
Using a locally cached version of GPL6947 found here:
C:\Users\Sharon\AppData\Local\Temp\RtmpmaCHbX/GPL6947.soft.gz 
Error in readLines(con, 100) : error reading from the connection
In addition: Warning message:
In for (f in filters) { :
  closing unused connection 3 (C:\Users\Sharon\AppData\Local\Temp\RtmpmaCHbX/GPL6947.soft.gz)

Would really appreciate help in understanding and solving this issue. I have used this code: gse=getGEO(my_id)

Thank you

R GEO • 392 views
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Entering edit mode

Hi Sharon,

What tutorial and package are you using to download the data?

Sam

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Entering edit mode

Hi Sam, Sorry for the late reply. Here is the tutorial : https://sbc.shef.ac.uk/geo_tutorial/tutorial.nb.html and I am using GEOquery.

Thank you.

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Entering edit mode
6 weeks ago

Upgrading to the most recent version of R (4.1 or later) and then reinstalling GEOquery should fix the issue. In particular, you'll be looking for GEOquery to be version 2.62.1 or later.

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Ok thank you so much Sean

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