在用Seurat包做多样本整合的时候，我们通常采用两种方式： （1）merge的方式 （2）FindIntegrationAnchors的方式整合 这里我们来解析一下FindIntegrationAnchors函数里面的参数及用法： 对于要进行多样本整合的数据，通常的做法是：也就是单样本做了均一化后，进行多样本的整合 那这个函数FindI...
展开全部 典型关联分析(Canonical Correlation Analysis,以下简称CCA)是最常用的挖掘数据关联关系的算法之一。比如我们拿到两组数据,第一组是人身高和体重的数据,第二组是对应的跑步能力和跳远能力的数据。那么我们能不能说这两组数据是相关的呢?CCA可以帮助我们分析这个问题。 在数理统计里面,我们都知道相关系数这个概...
Hi, I have about 5000 cells and 30 batches (or samples). I want to integrate them and remove the batch effect using FindIntegrationAnchors() and IntegrateData(). But there are less than 30 cells in some batch, so if I run: seu.anchors <-...
Hi all, I'm currently running into an issue when I try to use the FindIntegrationAnchors program with Seurat v3 where I get a subscript out of bounds error message. I've confirmed that everything works fine when I use the provided datase...
How do I analysis findmarkers and DEGs after integration with SCTtrasnform · Issue #3839 · satijalab/seurat (github.com)github.com/satijalab/seurat/issues/3839 3.Run "FindIntegrationAnchors" and "IntegrateData". Here I set the "features.to.integrate" to all gene, because I want to ...
在用Seurat包做多样本整合的时候,我们通常采用两种方式: (1)merge的方式 (2)FindIntegrationAnchors的方式整合 这里我们来解析一下FindIntegrationAnchors函数里面的参数及用法: 对于要进行多样本整合的数据,通常的做法是: for(eachinsamples){# ob=paste("ob",each,sep="_")pbmc<-readRDS(paste0(path,'/',each...
hi 各位,今天我们来深入了解一下Seurat做多样本整合的深入算法,CCA算法以及FindIntegrationAnchors函数中的的参数l2.norm 先来知道一下CCA 典型关联分析(Canonical Correlation Analysis,以下简称CCA)是最常用的挖掘数据关联关系的算法之一。比如我们拿到两组数据,第一组是人身高和体重的数据,第二组是对应的跑步能力和跳远...
I am trying to analyze Covid 19 data sets from 17 different labs. When I was trying to find integration anchors, with the following code: pbmc.anchors=FindIntegrationAnchors(object.list=pbmc.list,anchor.features=features,reduction="rpca"...
I got the error they got, except when running FindIntegrationAnchors(). combo <- merge(sobj_tnbc, y = c(sobj_ER, sobj_her, sobj_lumb), add.cell.ids = c("TNBC", "ER", "HER","ERHER")) head(combo@meta.data) combo.split <- SplitObject(combo, split.by = "Patient") combo...
用SCT标准化,FindIntegrationAnchors做了去批次。作者在做完FindClusters之后,关键的两步是DefaultAssay(objs) <- 'SCT' 和objs<- PrepSCTFindMarkers(objs,assay = "SCT", verbose = TRUE) 贴一下作者的代码: 先按照这个跑一下看看 library(Seurat) library(tidyverse) library(ggplot2) library(ggsci) library(...