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ByrumLab / ProteoViz

Interactive tool for Phosphoproteomics
Apache License 2.0
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S5_Run_PTMSig Erro message #1

Open cmysrobinso opened 4 years ago

cmysrobinso commented 4 years ago

Hi,

I'm a bit new to R so please excuse my ignorance, and I am trying to run your example dataset to learn the package. When I run the S5_Run_PTMSig... script I keep getting the error:

Error in ssGSEA2(gct_file, gene.set.databases = sig_db, sample.norm.type = sample.norm.type, : object 'm' not found

I'm a bit stuck after trying to troubleshoot without luck and any advice would be wonderful. Thank you.

AaronStorey commented 4 years ago

Hi cmysrobinso,

This error may occur if the path to the gct_file object isn't pointing to the relative location of the "phospho_PTMsig_input.gct" file. If you are running this interactively, try running the "S5_Run_PTMsig_ssGSEA.R" script line-by-line until the last line, then:

file.exists(gct_file)

If false, then that object needs to point to the phospho .gct file that was made in the "S4_Make_PTMsig_gct_input.R" script. If the above is true, then this file may not be a valid .gct file. Let me know, and I'll try to help figure out what's happening. I'm new to Github and debugging, but I'll help as best as I can.

There are a few calls and assignments to an object m in the "ssGSEA2.0" script, so this will be a matter of figuring out why that isn't being correctly assigned.