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andreasmock / MetaboDiff

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error with outlier function #5

Open Bela1229 opened 5 years ago

Bela1229 commented 5 years ago

Hello Dr. Mock, Thanks for providing the R package! I have been having issues running my data from Metabolon: outlier_heatmap(met1, group_factor="ONCO_ORAL_C2", label_colors=c("darkseagreen","dodgerblue"), k=2) Error in apply(assays(met)[["imputed"]], 1, median) : dim(X) must have a positive length

na_heatmap(met1, group_factor="ONCO_ORAL_C2", label_colors=c("darkseagreen","dodgerblue")) Error in colorRamp2(seq(min(matrix, na.rm = TRUE), max(matrix, na.rm = TRUE), : You should have at least two distinct break values.

(met1 <- remove_cluster(met1,cluster=1)) Error in apply(assays(met)[["imputed"]], 1, median) : dim(X) must have a positive length (met1 <- normalize_met(met1)) Error in colnames<-(*tmp*, value = colnames(raw_temp)) : attempt to set 'colnames' on an object with less than two dimensions

I noticed in my previous step met1 <- create_mae(assay1, rowData1, colData1) Warning messages: 1: In MultiAssayExperiment(experiments = experiment_list, colData = colData, : sampleMap[['primary']] coerced to character() 2: In MultiAssayExperiment(experiments = experiment_list, colData = colData, : sampleMap[['colname']] coerced to character()

I am using a couple of dataset as your example, and any help would be appreciated!@andreasmock

r-melo commented 4 years ago

Hi @Bela1229, I am having the same problems. did you happen to solve your issue?

Bela1229 commented 4 years ago

Hello, Thanks for reaching out. I do not think my problem ever got replied.

On Tue, Dec 3, 2019 at 2:28 PM r-melo notifications@github.com wrote:

Hi @Bela1229 https://github.com/Bela1229, I am having the same problems. did you happen to solve your issue?

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