ctlab / phantasus

Visual exploratory analysis of gene expression data
https://alserglab.wustl.edu/phantasus/
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Proxy Error #157

Closed Celia5 closed 4 years ago

Celia5 commented 4 years ago

I receive a Proxy Error every time I try to run an FGSEA on my RNA-seq data. When I analyzed this data using phantasus several months ago there was no issue. I have tried running the FGSEA on different computers, browsers, wifi networks, etc but keep getting this error:

Failed to perform FGSEA. Error: Proxy Error The proxy server received an invalid response from an upstream server. The proxy server could not handle the request POST /phantasus/ocpu/library/phantasus/R/performFGSEA/print. Reason: Error reading from remote server


Apache/2.4.18 (Ubuntu) Server at artyomovlab.wustl.edu Port 443

assaron commented 4 years ago

That's very strange. Can you please do the following:

  1. Open https://artyomovlab.wustl.edu/phantasus/?preloaded=GSE53986.Ctrl.vs.LPS
  2. Run FGSEA with MSigDB Hallmarks - Mus Musculus (Entrez) as pathway database, t as statistics and Gene ID as column with Gene IDs.

If it fails, please do the same for https://artyomovlab.wustl.edu/phantasus-dev/?preloaded=GSE53986.Ctrl.vs.LPS and for https://ctlab.itmo.ru/phantasus/?preloaded=GSE53986.Ctrl.vs.LPS

Celia5 commented 4 years ago

Hello,

When I try to run the FGSEA using the datasets you provided, it works just fine.

However when I try it on my dataset (either as a .gct or starting fresh from importing the original .tsv file) I receive either a "504 gateway timeout" error if I try using entrezgene or ensemble geneIDs as the Gene ID column, or a "FGSEA returned 0 rows. Nothing to show" error if I use the gene name. These are human genes but when I ran FGSEA a few months ago using the "gene name" it worked just fine using various databases.


From: Alexey Sergushichev notifications@github.com Sent: Saturday, September 19, 2020 2:57 AM To: ctlab/phantasus phantasus@noreply.github.com Cc: Cubitt, Celia celia.cubitt@wustl.edu; Author author@noreply.github.com Subject: Re: [ctlab/phantasus] Proxy Error (#157)

That's very strange. Can you please do the following:

  1. Open https://artyomovlab.wustl.edu/phantasus/?preloaded=GSE53986.Ctrl.vs.LPS
  2. Run FGSEA with MSigDB Hallmarks - Mus Musculus (Entrez) as pathway database, t as statistics and Gene ID as column with Gene IDs.

If it fails, please do the same for https://artyomovlab.wustl.edu/phantasus-dev/?preloaded=GSE53986.Ctrl.vs.LPS and for https://ctlab.itmo.ru/phantasus/?preloaded=GSE53986.Ctrl.vs.LPS

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ctlab/phantasus/issues/157#issuecomment-695193258, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARBXUBWGNSWEAOA2K3IKPH3SGR6CPANCNFSM4RSS6JCQ.

assaron commented 4 years ago

Ok, can you attach the dataset? If you don't want to make it public, you can send it to my e-mail (alsergbox@gmail.com)

assaron commented 4 years ago

The issue has been resolved