copykat issue: error in step 4

[YubinXie]

I have tried running with multiple sessions with my 70k cell data and I constantly get this error:

[1] "running copykat v1.1.0" [1] "step1: read and filter data ..." [1] "22318 genes, 73901 cells in raw data" [1] "8197 genes past LOW.DR filtering" [1] "step 2: annotations gene coordinates ..." [1] "start annotation ..." [1] "step 3: smoothing data with dlm ..." [1] "step 4: measuring baselines ..." [1] "23535 known normal cells found in dataset" [1] "run with known normal..." [1] "baseline is from known input" WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: Error in hclust(d, method = "ward.D2") : size cannot be NA nor exceed 65536 Calls: -> -> copykat -> hclust

[longyingda]

copykat calls the hclust function and specifies the "ward.D" method for analysis. It is possible that you have too many genes, so you can filter for genes with less than 3 (or more) expressed cells to reduce the number of genes.

in copykat call hclust（）： if(distance=="euclidean"){ ... hcc <- hclust(parallelDist::parDist(t(mat.adj),threads =n.cores, method = distance), method = "ward.D") }else { hcc <- hclust(as.dist(1-cor(mat.adj, method = distance)), method = "ward.D") ... }

but in hclust()

hclust function{ ... n <- as.integer(attr(d, "Size")) if(is.null(n)) stop("invalid dissimilarities") if(is.na(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") ... }

[YubinXie]

copykat calls the hclust function and specifies the "ward.D" method for analysis. It is possible that you have too many genes, so you can filter for genes with less than 3 (or more) expressed cells to reduce the number of genes.

in copykat call hclust（）： if(distance=="euclidean"){ ... hcc <- hclust(parallelDist::parDist(t(mat.adj),threads =n.cores, method = distance), method = "ward.D") }else { hcc <- hclust(as.dist(1-cor(mat.adj, method = distance)), method = "ward.D") ... }

but in hclust()

hclust function{ ... n <- as.integer(attr(d, "Size")) if(is.null(n)) stop("invalid dissimilarities") if(is.na(n) || n > 65536L) stop("size cannot be NA nor exceed 65536") ... }

Thanks for the reply. I figured it out. The clustering method limits the cell number below 65K. So one has to reduce the cell number.