Error: object 'plot_df' not found in IdentifyVaryingPWs()

[zhangjiaobxy]

Hello, I got an error of object 'plot_df' not found in IdentifyVaryingPWs() as below:

> cortex_tempora <- IdentifyVaryingPWs(cortex_tempora, pval_threshold = 0.05)
Fitting GAM models...Error in IdentifyVaryingPWs(cortex_tempora, pval_threshold = 0.05) : 
  object 'plot_df' not found

I am using the tutorial MouseCortex.RData data. I am using Mouse_GOBP_AllPathways_no_GO_iea_April_01_2020_symbol.gmt in function CalculatePWProfiles(), because I can not find the Mouse_GOBP_AllPathways_no_GO_iea_September_01_2019_symbol.gmt file on the website (http://download.baderlab.org/EM_Genesets/current_release/).

Any help will be appreciated, thanks a lot!

[risserlin]

not sure if I can help with the running error but you can find the gmt file specified in this directory: http://download.baderlab.org/EM_Genesets/September_01_2019/Mouse/symbol/

here is a link to the file: http://download.baderlab.org/EM_Genesets/September_01_2019/Mouse/symbol/Mouse_GOBP_AllPathways_no_GO_iea_September_01_2019_symbol.gmt

[zhangjiaobxy]

Thanks for your help!

I tried this file (Mouse_GOBP_AllPathways_no_GO_iea_September_01_2019_symbol.gmt) as described in the tutorial. But I still get the same error for one of my datasets. However, IdentifyVaryingPWs() works for some of the datasets. Does that error indicate there is no varying pathways detected, so the code can't plot any figure?

[thinh-tran]

Hi! My apology for the late response. The error you received can be due to Tempora not detecting any varying pathways as you said. I have fixed the error messages so that it's clearer if this happens.