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bigomics / omicsplayground

Visual self-service analytics platform for big omics data.
http://www.bigomics.ch
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Error in contrasts<-: contrasts can be applied only to factors with 2 or more levels #1227

Open zitoa opened 1 month ago

zitoa commented 1 month ago

HS Ticket: 15965137125

Warning: Error in contrasts<-: contrasts can be applied only to factors with 2 or more levels 200: h 199: .handleSimpleError 198: stop 197: contrasts<- 196: model.matrix.default 195: model.matrix 194: runBatchCorrectionMethods 193: playbase::compare_batchcorrection_methods 192: eval 191: eval 190: shiny::withProgress 189: 188: ..stacktraceon.. 187: .func 186: withVisible 185: withCallingHandlers 184: contextFunc 183: env$runWith 182: force 181: domain$wrapSync 180: promises::with_promise_domain 179: withReactiveDomain 178: domain$wrapSync 177: promises::with_promise_domain 176: ctx$run 175: self$.updateValue 174: ..stacktraceoff.. 173: results_correction_methods 172: plot_all_methods 171: func 170: renderPlot 169: ..stacktraceon.. 168: func 167: force 166: withVisible 165: withCallingHandlers 164: domain$wrapSync 163: promises::with_promise_domain 162: captureStackTraces 161: doTryCatch 160: tryCatchOne 159: tryCatchList 158: tryCatch 157: do 156: hybrid_chain 155: force 154: domain$wrapSync 153: promises::with_promise_domain 152: force 151: withVisible 150: withCallingHandlers 149: domain$wrapSync 148: promises::with_promise_domain 147: captureStackTraces 146: doTryCatch 145: tryCatchOne 144: tryCatchList 143: tryCatch 142: do 141: hybrid_chain 140: force 139: withVisible 138: withCallingHandlers 137: domain$wrapSync 136: promises::with_promise_domain 135: captureStackTraces 134: doTryCatch 133: tryCatchOne 132: tryCatchList 131: tryCatch 130: do 129: hybrid_chain 128: drawPlot 127: do.call 126: force 125: withVisible 124: withCallingHandlers 123: domain$wrapSync 122: promises::with_promise_domain 121: captureStackTraces 120: doTryCatch 119: tryCatchOne 118: tryCatchList 117: tryCatch 116: do 115: hybrid_chain 114: 113: ..stacktraceon.. 112: .func 111: withVisible 110: withCallingHandlers 109: contextFunc 108: env$runWith 107: force 106: domain$wrapSync 105: promises::with_promise_domain 104: withReactiveDomain 103: domain$wrapSync 102: promises::with_promise_domain 101: ctx$run 100: self$.updateValue 99: ..stacktraceoff.. 98: drawReactive 97: force 96: withVisible 95: withCallingHandlers 94: domain$wrapSync 93: promises::with_promise_domain 92: captureStackTraces 91: doTryCatch 90: tryCatchOne 89: tryCatchList 88: tryCatch 87: do 86: hybrid_chain 85: renderFunc 84: output$upload-checkqc-plot4-renderfigure 83: ..stacktraceon.. 82: orig 81: func 80: withCallingHandlers 79: domain$wrapSync 78: promises::with_promise_domain 77: captureStackTraces 76: withCallingHandlers 75: shinyCallingHandlers 74: force 73: domain$wrapSync 72: promises::with_promise_domain 71: private$withCurrentOutput 70: force 69: withVisible 68: withCallingHandlers 67: domain$wrapSync 66: promises::with_promise_domain 65: captureStackTraces 64: doTryCatch 63: tryCatchOne 62: tryCatchList 61: tryCatch 60: do 59: hybrid_chain 58: force 57: withVisible 56: withCallingHandlers 55: domain$wrapSync 54: promises::with_promise_domain 53: captureStackTraces 52: doTryCatch 51: tryCatchOne 50: tryCatchList 49: tryCatch 48: do 47: hybrid_chain 46: observe 45: <observer:output$upload-checkqc-plot4-renderfigure> 44: contextFunc 43: env$runWith 42: force 41: domain$wrapSync 40: promises::with_promise_domain 39: withReactiveDomain 38: domain$wrapSync 37: promises::with_promise_domain 36: ctx$run 35: run 34: withCallingHandlers 33: domain$wrapSync 32: promises::with_promise_domain 31: captureStackTraces 30: withCallingHandlers 29: shinyCallingHandlers 28: force 27: withVisible 26: withCallingHandlers 25: domain$wrapSync 24: promises::with_promise_domain 23: captureStackTraces 22: doTryCatch 21: tryCatchOne 20: tryCatchList 19: tryCatch 18: do 17: hybrid_chain 16: flushCallback 15: FUN 14: lapply 13: ctx$executeFlushCallbacks 12: .getReactiveEnvironment()$flush 11: flushReact 10: serviceApp 9: ..stacktracefloor.. 8: withCallingHandlers 7: domain$wrapSync 6: promises::with_promise_domain 5: captureStackTraces 4: ..stacktraceoff.. 3: runApp 2: print.shiny.appobj 1:

zitoa commented 1 month ago

When using all 4 contrasts, error in compare_batchcorrection_methods >> get_model_parameters resulting to pars$batch, pars$pheno, pars$batch.pars, pars$pheno.pars all NULL. No replicates when combining phenotypes - duplication of samples occurs in gx.limmaF. Under assessment.