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jdrudolph / photon

PHOsphoproteomic dissecTiOn using Networks
GNU General Public License v3.0
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Error message for network analysis #33

Open bstankavich opened 4 years ago

bstankavich commented 4 years ago

Hi!

I keep getting an error during step 2 in Create the PPI network from the edge table and prepare it for data annotation. I have the matrix of the protein-protein interactions open and am trying to transform it into the "Network collection" data structure by selecting Network → From matrix → Basic → From matrix and choosing protein1 and protein2 as 'Source' and 'Target', and checking the Network is directed option. When I click OK, I get the following error message:

image

I've tried installing the latest version of Perseus (v1.6.14.0) but the same error occurs. Any help would be much appreciated!

masaver commented 4 years ago

Hi!

I keep getting an error during step 2 in Create the PPI network from the edge table and prepare it for data annotation. I have the matrix of the protein-protein interactions open and am trying to transform it into the "Network collection" data structure by selecting Network → From matrix → Basic → From matrix and choosing protein1 and protein2 as 'Source' and 'Target', and checking the Network is directed option. When I click OK, I get the following error message:

image

I've tried installing the latest version of Perseus (v1.6.14.0) but the same error occurs. Any help would be much appreciated!

Hi!,

I just encountered the same error you describe . Any luck on finding a way to fix it ?

Cheers,

-Mathias

bstankavich commented 4 years ago

Unfortunately, no luck yet. Hoping that @jdrudolph may be able to help.

IsalineMs commented 4 years ago

Hi guys,

I had the same error message on the version 1.6.14.0. of perseus. I got it to work by using another Perseus version (still had 1.6.7.0 on my computer). Good luck!

Menoetes commented 3 years ago

Hello,

I get a similar error message in Perseus 1.6.2.3. , in 1.6.14. I can't get past creating a network from matrix step.

Best wishes, Tilen

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WebbYang commented 3 years ago

Hi,

Is there any available Perseus version can be downloaded without this error? I've tried from v.1.6.10.50, v.1.6.10.40 and v1.6.15.0 and none can work.

Thanks Webb

john-mcmanus commented 3 years ago

I've also just hit this issue!

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john-mcmanus commented 3 years ago

I've also just hit this issue!

image

Solved this just by updating to the latest version! I was running 1.6.14.0 - I just downloaded 1.6.15.0 and replaced my current Perseus version, and the same command worked with no issues.

WebbYang commented 3 years ago

Solved this just by updating to the latest version! I was running 1.6.14.0 - I just downloaded 1.6.15.0 and replaced my current Perseus version, and the same command worked with no issues.

Good to here that you worked! But my 1.6.15.0 still can't work.

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john-mcmanus commented 3 years ago

Solved this just by updating to the latest version! I was running 1.6.14.0 - I just downloaded 1.6.15.0 and replaced my current Perseus version, and the same command worked with no issues.

Good to here that you worked! But my 1.6.15.0 still can't work.

image

Strange. I don't really know enough about it to give you any good answers - for me I just downloaded the most recent version of Perseus, extracted the .zip file, copied the contents into "C:\Program Files (x86)\Perseus 1.6.14.0" replacing all existing files of the same name with the new files I was copying in, then I changed the name of the folder to "Perseus 1.6.15.0". This felt a bit clunky but it didn't want to automatically replace existing files!

Best of luck & apologies I couldn't be more helpful there.

danielaferretti1992 commented 3 years ago

Hi All, so we released last January (2021) Perseus 1.6.15.0 and it seems that for @john-mcmanus it works. @bstankavich @IsalineMs @Menoetes please tell us if it works for you. @WebbYang do you have the same issue in the same step? (from Matrix)

Best, Daniela

john-mcmanus commented 3 years ago

Hi All, so we released last January (2021) Perseus 1.6.15.0 and it seems that for @john-mcmanus it works. @bstankavich @IsalineMs @Menoetes please tell us if it works for you. @WebbYang do you have the same issue in the same step? (from Matrix)

Best, Daniela

Hi @danielaferretti1992 - can confirm that this was working for me. I have had other issues though that still seem to be unaddressed? (https://github.com/jdrudolph/photon/issues/27) Sorry for jumping in with the off topic - it would be great to get it working! Thanks, John

rjmusich commented 3 years ago

Hi All, so we released last January (2021) Perseus 1.6.15.0 and it seems that for @john-mcmanus it works. @bstankavich @IsalineMs @Menoetes please tell us if it works for you. @WebbYang do you have the same issue in the same step? (from Matrix)

Best, Daniela

@danielaferretti1992 I am also encountering this same issue running Perseus 1.6.15.0 downloaded directly from source. Seems like maybe the only way around this error is @john-mcmanus way of having a previous version of Perseus downloaded and copying the files from v1.6.15.0 to the old installation? I have not tried this yet, but that seems to me that something got removed from version 1.6.14.0 that is not present in v1.6.15.0 so copying the files from v1.6.15.0 to the v1.6.14.0 folder would keep all files unique to v1.6.14.0 and update all files that are the same between versions. Seems like those files that are unique to v1.6.14.0 may be required to keep Photon running...

Is there any way for me to install a previous version of Perseus (specifically v1.6.14.0) to confirm that John's method of fixing this isn't just unique to their machine?

Menoetes commented 3 years ago

Hi all,

it works for me in 1.6.15.0, thank you very much!

All best, Tilen