Error in Creating CDS object for Garnett with Monocle 3: (Error: is(object = cds, class2 = "CellDataSet") is not TRUE)

[marwaabdelazim]

The code i used:

First install Bioconductor and Monocle

if (!requireNamespace("BiocManager")) install.packages("BiocManager")

BiocManager::install() BiocManager::install(c("monocle"))

Next install a few more dependencies

BiocManager::install(c('DelayedArray', 'DelayedMatrixStats', 'org.Hs.eg.db', 'org.Mm.eg.db')) library(monocle)

install.packages("devtools") devtools::install_github("cole-trapnell-lab/garnett", force = TRUE)

library(garnett)

devtools::install_github("cole-trapnell-lab/garnett", ref="monocle3")

To check garnett version

packageDescription("garnett")$Version

library(Seurat) library(monocle3) install.packages(monocle3)

First install Bioconductor and Monocle 3

if (!requireNamespace("BiocManager")) install.packages("BiocManager")

BiocManager::install()

Next install a few more dependencies

BiocManager::install(c('BiocGenerics', 'DelayedArray', 'DelayedMatrixStats', 'limma', 'S4Vectors', 'SingleCellExperiment', 'SummarizedExperiment'))

install.packages("devtools") devtools::install_github('cole-trapnell-lab/monocle3') library(monocle3)

read query

Querydata <- readRDS("D:/Multiple Myeloma project/ANNOTATION STEP BY TREEARCHES TOOL/garnet/final_Downsample_RCPA.rds")

Integrated assay has zero couunts so i switch to RNA assay

DefaultAssay(object = Querydata) <- "RNA"

Create cds object

qdata <- GetAssayData(object = Querydata, slot = "counts") celldata <- as.data.frame(Querydata@meta.data) genedata <- as.data.frame(x = row.names(Querydata), row.names = row.names(Querydata)) colnames(genedata) <- "gene_short_name"

cds <- new_cell_data_set(qdata, cell_metadata = celldata, gene_metadata = genedata)

classifier <- readRDS("D:/Multiple Myeloma project/ANNOTATION STEP BY TREEARCHES TOOL/garnet/ceWhole_20191017.RDS")

library(org.Hs.eg.db)

classify your cells

MM_cds <- classify_cells(cds, classifier, db = org.Hs.eg.db, cluster_extend = FALSE, cds_gene_id_type = "SYMBOL")

Error: is(object = cds, class2 = "CellDataSet") is not TRUE

[hpliner]

Hello, sorry for the delay. Monocle and Monocle3 are not compatible and it looks like you're loading both here. Try restarting your session and only loading monocle3 and garnett, (i.e. no library(monocle)). I think that should solve your issue.