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DEG1 analysis crashes #667

Open Alib144 opened 4 weeks ago

Alib144 commented 4 weeks ago

IDEP 2.01 crashes during the DEG1 step. As soon as you hit 'Submit', it says: "The application unexpectedly exited. Diagnostic information is private. Please ask your system admin for permission if you need to check the R logs."

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Biomicrogen commented 2 weeks ago

similar issue which seems like it has to do with the way idep is handling multiple comparisons via the interactions matrix. Rstudio error below: "Warning: Error in checkFullRank: the model matrix is not full rank, so the model cannot be fit as specified. One or more variables or interaction terms in the design formula are linear combinations of the others and must be removed.

Please read the vignette section 'Model matrix not full rank':

vignette('DESeq2') 3: runApp 2: print.shiny.appobj 1: "

Alib144 commented 2 weeks ago

similar issue which seems like it has to do with the way idep is handling multiple comparisons via the interactions matrix. Rstudio error below: "Warning: Error in checkFullRank: the model matrix is not full rank, so the model cannot be fit as specified. One or more variables or interaction terms in the design formula are linear combinations of the others and must be removed.

Please read the vignette section 'Model matrix not full rank':

vignette('DESeq2') 3: runApp 2: print.shiny.appobj 1: "

Thanks a lot for the info! I've found that, if you leave the default comparison settings alone and run it immediately, it will work without crashing. After this initial run, you can then go back and change to the comparisons that you actually want and run it again with no crashing issue. It's a very weird error; I've gotten it with multiple different datasets--including some that I had previously run on IDEP.96 and IDEP2.01 for years with no problems. I've also encountered the crashing with datasets that I obtained from NCBI GEO.