eset2Phase error

[minghao622]

Hello,

I am reaching out to ask for your help regarding an issue I encountered while using your toolkit, specifically with the function Est2Phase(SingleCellExperiment::SingleCellExperiment(assays = total_matrix_filter)). Here’s a brief summary of what I did:

First, I constructed the design matrix with the following code:

design=data.frame(row.names = colnames(total_matrix_filter),
                  condition=factor(stringr::str_split(colnames(total_matrix_filter),pattern = "_",simplify = T)[,1] , levels=c("T38","T28"))
                 )
phenoData <- new("AnnotatedDataFrame", data=design)
eset2Phase(ExpressionSet(assayData=total_matrix_filter, phenoData=phenoData),)

Afterwards, when running eset2Phase, I received repeated warnings like:

“Warning message in RobustPoi0(yy): ‘Proportion of zero inflation is negative’”

Which eventually led to this error:

Error in if (any(p0 < 0)) {: missing value where TRUE/FALSE needed

Could you please advise on possible causes and suggest how to resolve this error? If necessary, I can provide more data or a minimal reproducible example to help diagnose the problem.

Thank you very much for developing this tool and for taking the time to review my issue. I look forward to your guidance.

Best regards