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UCSF-DSCOLAB / cyclone

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Issue Report - Error in Step 7 #15

Open CeliaJuarillo opened 8 months ago

CeliaJuarillo commented 8 months ago

I hope this message finds you well. I am currently using your package for spectral cytometry analysis, I have encountered some errors along the way but I was able to solved them but now I have encountered an issue in Step 7.

Starting step#: 7 [1] "Markers used for SCAFFoLD: CD45RA, CD8, CCR7, CD3, CD4, CD25, CD56, CD127, HLADR, CD38" [1] "Using as reference Panel_Pep_Javier T+NK 230124-BL_01 CNT-ALL BL-1 CONTROL_Unmixed.fcs.clustered.txt" [1] "Downsampling to 1000 events" [1] "Processing /home/cjuarez/Escritorio/spectral/cyclone_new/outputs/scaffold/Panel_Pep_Javier T+NK 230124-BL_01 CNT-ALL BL-1 CONTROL_Unmixed.fcs.clustered.txt" [1] "Running with Edge weight: 4.000000" Error in [.data.frame(tab, , col.names) : undefined columns selected Calls: ... process_data -> build_graph -> as.matrix -> [ -> [.data.frame Además: Warning messages: 1: replacing previous import ‘flowCore::normalize’ by ‘igraph::normalize’ when loading ‘scaffold’ 2: replacing previous import ‘plyr::rename’ by ‘reshape::rename’ when loading ‘scaffold’ 3: replacing previous import ‘plyr::round_any’ by ‘reshape::round_any’ when loading ‘scaffold’ 4: '.local' is deprecated. Use 'keyword' instead. See help("Deprecated") Ejecución interrumpida

I don't know where is the problem, since this step requires the scaffold package I have tried to uninstall it and install it again but it's not working. I don't know if it has something to do with the files that have been created through the other steps or with my fcs files.

I hope you can help me with this.

ravipatel4 commented 8 months ago

@CeliaJuarillo, were you able to resolve the issue? I am unable to see any description of your issue.

CeliaJuarillo commented 8 months ago

@CeliaJuarillo, were you able to resolve the issue? I am unable to see any description of your issue.

Sorry I changed it cause I was able to resolve the first issue but now I have encountered another one.

ravipatel4 commented 7 months ago

Hi @CeliaJuarillo, running SCAFFoLD is an optional step. If you exclude the gated fcs files input in config.yml (gated_fcs_dir: ""), it will skip the SCAFFoLD step. But if you want to run this step, please make sure the channel names match between the FCS files you loaded during the first step and the FCS files in gated fcs files input. If this does not resolve the issue please send us another message. Re. changing your message, please post a new comment to the existing issue so that we can keep track of all the communications for the future reference. Thank you.