RPX PXDataset error
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@47a84d4e
Last seen 5 weeks ago
Spain

Enter the body of text here

Code should be placed in three backticks as shown below


 library("rpx")
 px1 <- PXDataset("PXD000001")
Querying ProteomeXchange for PXD000001.
Error in file(file, "rt") : 
  cannot open the connection to 'ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/README.txt'
In addition: Warning message:
In file(file, "rt") :
  URL 'ftp://ftp.pride.ebi.ac.uk/pride-archive/2012/03/PXD000001/README.txt': status was 'Couldn't connect to server'

Hello, I am doing a tutorial about Quantitative Proteomics using rpx to import data and PXDataset keeps giving me error in fpt connexion. Is there any way to load all needed data into "px1" without the need to download it from fpt? I downloaded all needed files in local. I both tried from behind a firewall and not.

Thank you very much for your help

Gianluigi

PRIDE rpx PXDataset • 149 views
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Sakimmd7 • 0
@35cba962
Last seen 5 weeks ago
United Kingdom

Hi Gianluigi,

I am doing the same course currently and stumbled upon the same issue. After trying out different things, I realised the problem is with the data file itself rather than the code. So I am doing the tutorial with another data (PXD029754) and it is working. Hope this helps.

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@laurent-gatto-5645
Last seen 9 days ago
Belgium
  • From the URL in the error, it looks like you have the latest (or a recent) rpx version. It is generally recommended to add the output of sessionInfo() to confirm that.
  • PRIDE has had connection issues for a long time, and there still are some occasionally, so I would suggest to try again - you can check that the URL does exists and is (when I tested at least) accessible.
  • And if PXD000001 fails, as suggested, you can use other ones - here, in section 4.8, you'll find an exercise with PXD022816.
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