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wenweixiong / MARVEL

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An error of function "adhocGene.TabulateExpression.PSI.10X" #13

Closed ksbb1853223 closed 1 year ago

ksbb1853223 commented 1 year ago

Dear wenweixiong: I used Marvel to analyze "ADCY7" genes.The function” adhocgene.tabulateexpression.10x“ worked fine. But there was an error when using the function "adhocGene.TabulateExpression.PSI.10X".The error message is ”Error in aggregate.data.frame(as.data.frame(x), ...) : no rows to aggregate“.

The code comes from the official site guide, and I only changed the gene name and min.pct.cells. marvel <- adhocGene.TabulateExpression.Gene.10x(MarvelObject=marvel, cell.group.list=cell.group.list, gene_short_name="ADCY7", min.pct.cells = 1) marvel <- adhocGene.TabulateExpression.PSI.10x(MarvelObject=marvel, min.pct.cells=1)

When I replace Adcy7 with S100A8, the error disappears. And how to resolve ADCY7 encountered errors. Thanks!

ksbb1853223 commented 1 year ago

I re-adjusted the ”min.pct.cells“ values and it worked fine

wenweixiong commented 1 year ago

ADCY7 was probably a very lowly-expressed gene, i.e. expressed in <1% of the cells of your dataset.