几天前,曾老师在群里给我布置了一份学徒作业,比较不同流程(limma/voom,edgeR,DESeq2 )差异分析的区别,拟使用的数据集是TCGA-BRCA的counts值矩阵。...(dds, contrast = c("condition",rev(levels(group_list))))
resOrdered 值排序...=edgeR_DEG[,1:2]
head(td1)
colnames(td1)=c("logFC_edgeR","logCPM_edgeR")
td1$ID=rownames(td1)
td2=limma_voom_DEG...[,1:2]
head(td2)
colnames(td2)=c("logFC_limma","logCPM_limma")
td2$ID=rownames(td2)
td3=DESeq2_DEG[,...(td3,td2,by="ID")
td_DESeq2_limma=td_DESeq2_limma[,c(3,2,4)]
head(td_DESeq2_limma)
#选出500个logFC绝对值最大的