悬赏 5 个论坛币 未解决
以下是Bioconductor中GO分析代码:
library(GOstats)
library(hgu95av2.db)
library(hgu95av2)#为了保险加载了两个
entrezUniverse<- unique(unlist(mget(rownames(Dset),hgu95av2ENTREZID))) #提取芯片中所有ENTRIZID
entrezSelected<-unique(dif[!is.na(dif$EntrezID),"EntrezID"]) #提取差异表达基因对应ENTREZID
params<-new("GOHyperGParams",geneIds = entrezSelected, universeGeneIds = entrezUniverse,
annotation=affydb,, pvalueCutoff=0.001, conditional=FALSE,testDirection="over")
#params设计富集参数
hgOver<-hyperGTest(params) #超几何分布
bp<-summary(hgOver) #生成GO报表
htmlReport(hgOver,file='ALL_go.html') #生成检验文件结果
head(bp)
红色部分为出现问题的部分:
Dset是gcrma法处理后的芯片数据
Error: hgu95av2PFAM is defunct. Please use select() if you need access to PFAM or PROSITE accessions.> ****<-rownames(Dset)> entrezUniverse<- unique(unlist(mget(****,hgu95av2ENTREZID))) #提取芯片中所有ENTRIZIDError in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "1552256_a_at" not found> entrezSelected<-unique(dif[!is.na(dif$EntrezID),"EntrezID"]) #提取差异表达基因对应ENTREZID> params<-new("GOHyperGParams",geneIds = entrezSelected, universeGeneIds = entrezUniverse,+ annotation=affydb,, pvalueCutoff=0.001, conditional=FALSE,testDirection="over")Error in .nextMethod(.Object = .Object, ... = ...) : object 'entrezUniverse' not found。
“hgu95av2PFAM is defunct” 是不是因为hgu95av2PFAM失效了,如果失效应该怎么做?但是作为新手找不到问题所在。望高手指点。
shibushi hgu95av2PFAM is defunct