Hello everyone! I am working with the https://github.com/adamjamesreid/Plasmodium-single-cell-RNA-seq files. The first lines of the code are:

molecules <- read.table("PbM_counts.txt", sep = "\t", header = TRUE, row.names=1)

anno <- read.table("PbM_meta.txt", sep = "\t", header=TRUE)

genes <- read.table("berg.desc", header=FALSE, row.names=1, quote = "", sep="\t")

pheno_data <- new("AnnotatedDataFrame", anno)

rownames(pheno_data) <- pheno_data$sample_id

PbM <- SingleCellExperiment(assays = list(counts = as.matrix(molecules)),
                            colData = anno)

PbM$phenoData<- pheno_data

Now I need to deconvolute those data using bseq-sc package (https://shenorrlab.github.io/bseqsc/vignettes/bseq-sc.html). The first problem I have found is when I want to run the plotCellTotals with my data. This last command requires an ExpressionSet object, while my PbM is a SingleCellExperiment object. How can I make it work?

It makes very little sense to convert a SingleCellExperiment object to an ExpressionSet, because the former is intended for the task at hand, and the latter was originally intended for microarray data.

That said, the package you are asking about isn't a Bioconductor package, and this support site is for the support of Bioconductor packages, so this isn't the place to ask. If you have questions about the package, you should ask the authors, who would presumably know the answers.