Code should be placed in three backticks as shown below
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'
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.
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.
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.