Imputation function not working

[Januka-K]

First of all, thank you for this wonderful package.
The imputation function is not working. I have as many NAs after the imputation. Is there something that I need to take into consideration?

[WandrilleD]

I would like to add something on that because I have the same issues.
To be more specific, I think the function ptImpute does not work.

Using the code you provide in https://pyanglab.github.io/PhosR/articles/web/imputation.html

data("phospho.cells.Ins.pe")

ppe <- phospho.cells.Ins.pe 
class(ppe)

grps = gsub("_[0-9]{1}", "", colnames(ppe))

# FL38B
gsub("Intensity.", "", grps)[1:12]
# Hepa1
gsub("Intensity.", "", grps)[13:24]

dim(ppe)

ppe_filtered <- selectGrps(ppe, grps, 0.5, n=1) 
dim(ppe_filtered)

set.seed(123)
ppe_imputed_tmp <- scImpute(ppe_filtered, 0.5, grps)[,colnames(ppe_filtered)]

set.seed(123)
ppe_imputed <- ppe_imputed_tmp
ppe_imputed[,seq(6)] <- ptImpute(ppe_imputed[,seq(7,12)], 
                                 ppe_imputed[,seq(6)], 
                                 percent1 = 0.6, percent2 = 0, paired = FALSE)
ppe_imputed[,seq(13,18)] <- ptImpute(ppe_imputed[,seq(19,24)], 
                                     ppe_imputed[,seq(13,18)], 
                                     percent1 = 0.6, percent2 = 0, paired = FALSE)

original number of NAs:

sum( is.na( ppe_imputed_tmp@assays@data[["Quantification"]] ) )

[1] 15519

after first pass of imputation:

sum( is.na( ppe_imputed_tmp@assays@data[["imputed"]] ) )

[1] 10644

After ptImpute

sum( is.na( ppe_imputed@assays@data[["imputed"]] ) )

[1] 10644

So the second phase of imputation seems to have no impact, and we are stuck with NAs in the data.
Or is there something I am not understanding?