jitMarkerplt<-function(df,score="avg_log2FC",group="cluster",symbol="gene"){library(dplyr);library(ggplot2);library(BuenColors)df[,group]<-factor(df[,group],levels=sort(names(table(df[,group])))# 重新排序因子,决定坐标轴出图顺序if(sum(!is.na(as.numeric(names(table(df[,group])))!
base = 2 ) } treat.celltype.de <- lapply(treat.celltype.de, function(x) rownames_to_column(x, "Gene")) write_xlsx(treat.celltype.de, "treat.celltype.de.xls") yjchen1201mentioned this issueOct 10, 2023 FindAllMarkers returns different avg_log2FC values different Seurat versions#7862...
Question 2: Why I am not able to replicate the calculated avg_log2FC using snippets from the source code? Looking at the code, avg_log2FC is calculated directly from "total.diff" as according to the code: "to.return[, "avg_logFC"] <- total.diff[rownames(x = to.return)]". And...
Hi Seurat dev team, Thanks for the amazing work you have been doing to enable the community to perform single-cell data analysis. I have noticed discrepancies in FindMarkers outputs regarding the average log2FC values in the different te...
Now, here is the table of all markers. As you can see, the "avg_log2FC" column has very high numbers and "Inf" infinity values. Is there anything wrong and may I ask what should I do here? Copy link Collaborator timoastcommentedAug 27, 2021 ...
FindAllMarkers returns different avg_log2FC values between Seurat version 4.0.3 and 4.3.0. Cannot reproduce it on pbmc3k dataset though. Using in house data the differences are striking in avg_log2FC values and number of genes. Here is the code on in house data: ...
avg_log2FC pct.1 pct.2 p_val_adj#chr1-2471903-2481288 0.003694153 0.4647995 0.78 0.52 1results1['chr1-2471903-2481288', ]dat<-GetAssayData(atac_small,assay='peaks',slot='data') log2(mean(dat['chr1-2471903-2481288',cells1])+1)-log2(mean(dat['chr1-2471903-2481288',cells2]+1))...