Open fpengstudy opened 1 year ago
Hi, First, thanks for this usefor method! Second, when I use this tools, I meet some errors in step4
Here is my error:
Error in hclust(d, method = "ward.D2") : 大小不能是NA，出不能超出65536 Calls: copykat -> baseline.norm.cl -> hclust 停止执行
These are process:
soft hard 1e+05 Inf [1] "running copykat v1.1.0" [1] "step1: read and filter data ..." [1] "22701 genes, 71085 cells in raw data" [1] "filtered out 1048 cells with less than 200 genes; remaining 70043 cells" [1] "9514 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 ..."
And my code is below: library(tidyverse) library(copykat) library(ulimit)
ulimit::memory_limit(100000)
squ_epi <- readRDS("/public/home/fpeng/single_cell_R/R_result/squ_epi.rds") counts_squ_epi <- as.matrix(squ_epi@assays$RNA@counts) cnv_squ_epi <- copykat(rawmat = counts_squ_epi,ngene.chr = 5,sam.name = "SQU_EPI",distance="euclidean",n.cores = 4) save.image('/public/home/fpeng/single_cell_R/R_result/cnvimage.RData')
I would feel very privileged if you could answer my questions. Thanks again for you and your tools!
https://github.com/navinlabcode/copykat/issues/84#issue-1646109349
longyingda
commented
1 year ago longyingda
commented
1 year ago
Hi, First, thanks for this usefor method! Second, when I use this tools, I meet some errors in step4
Here is my error:
Error in hclust(d, method = "ward.D2") : 大小不能是NA，出不能超出65536 Calls: copykat -> baseline.norm.cl -> hclust 停止执行
These are process:
soft hard 1e+05 Inf [1] "running copykat v1.1.0" [1] "step1: read and filter data ..." [1] "22701 genes, 71085 cells in raw data" [1] "filtered out 1048 cells with less than 200 genes; remaining 70043 cells" [1] "9514 genes past LOW.DR filtering" [1] "step 2: annotations gene coordinates ..." [1] "start annotation ..." [1] "step 3: smoothing data with dlm ..." [1] "step 4: measuring baselines ..."
And my code is below: library(tidyverse) library(copykat) library(ulimit)
ulimit::memory_limit(100000)
scRNA2 <- readRDS("/public/home/fpeng/single_cell_R/R_result/scRNA2.Rds")
squ_epi <- readRDS("/public/home/fpeng/single_cell_R/R_result/squ_epi.rds") counts_squ_epi <- as.matrix(squ_epi@assays$RNA@counts) cnv_squ_epi <- copykat(rawmat = counts_squ_epi,ngene.chr = 5,sam.name = "SQU_EPI",distance="euclidean",n.cores = 4) save.image('/public/home/fpeng/single_cell_R/R_result/cnvimage.RData')
I would feel very privileged if you could answer my questions. Thanks again for you and your tools!