diff --git a/DESCRIPTION b/DESCRIPTION index 38bceae30..a6477e256 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: mia Type: Package -Version: 1.19.6 +Version: 1.19.7 Authors@R: c(person(given = "Tuomas", family = "Borman", role = c("aut", "cre"), email = "tuomas.v.borman@utu.fi", diff --git a/R/transformCounts.R b/R/transformCounts.R index 8ae315fdf..abb4e6e14 100644 --- a/R/transformCounts.R +++ b/R/transformCounts.R @@ -687,7 +687,9 @@ setMethod("transformAssay", signature = c(x = "SingleCellExperiment"), if( pseudocount && all(mat > 0, na.rm = TRUE) ){ pseudocount <- 0 message("The assay contains already only strictly positive ", - "values. Pseudocount is not added.") + "values. It is not recommended to add pseudocount", + "in such case. To force adding pseudocount you can", + "provide a numeric value for the pseudocount argument.") } # If pseudocount TRUE, set it to half of non-zero minimum value # else set it to zero.