On Tue, 30 May 2023 at 18:54, jmzvillarreal ***@***.***> wrote: I was able to fix the error by doing: sc_data <- ***@***.*** <https://github.com/CountS> sc_data <- Seurat_preprocessing(sc_data, min.cells= 1, min.features= 500, resolution= 0.2, dims_Neighbors= 1:20, dims_TSNE= 1:20, dims_UMAP= 1:20,verbose=TRUE) TCGA <- read.table('TCGA_status_ConsensusClass.txt', header = TRUE, sep = '\t',row.names = 1) TCGA <- TCGA[-c(1,2),] TCGA <- TCGA %>% mutate_all(as.numeric) metadata <- read.table('Subtype_info.csv', header = TRUE, sep = ',') all(colnames(TCGA) == metadata$Sample) TRUE table(metadata$genotype) NULL PRESENT 247 156 Execute Scissor to select the informative cells phenotype <-metadata$genotype tag <- as.list(phenotype) infos <- Scissor(as.matrix(TCGA), sc_data, phenotype,tag=tag, alpha = 0.2, family = "binomial") but now I am getting the following error: Error in Scissor(as.matrix(TCGA), sc_data, phenotype, tag = tag, : The length differs between tags and phenotypes. Please check Scissor inputs and selected regression type. In addition: Warning messages: 1: In asMethod(object) : sparse->dense coercion: allocating vector of size 17.8 GiB 2: In asMethod(object) : sparse->dense coercion: allocating vector of size 66.0 GiB 3: In Scissor(as.matrix(TCGA), sc_data, phenotype, tag = tag, : NAs introduced by coercion Any help would be appreciated ! — Reply to this email directly, view it on GitHub <#53 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEYQWDFAVX2LKKZOH7WKPCTXIXGWVANCNFSM6AAAAAAYQG6SO4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>