Error in contrasts<-: contrasts can be applied only to factors with 2 or more levels

[zitoa]

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: reactive:plotObj
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]

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.