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请会的老师能帮我看看吗?到QC.GUI就开始出错,是哪里出了问题吗?到SVD行的时候提示pd文件不对,这个数据集是不能用了吗?谢谢回答的战友
setwd("G:/geo")
library(ChAMP)
library(GEOquery)
gset <- getGEO('GSE46306', destdir=".",
AnnotGPL = F,
getGPL = F)
exprSet = exprs(gset[[1]])
head(exprSet)
pdata = pData(gset[[1]])
head(pdata) ###GEO数据加载后的查看
save(gset,file="exprSet")
CpG.GUI(CpG=rownames(exprSet),arraytype="450K")
QC.GUI(exprSet,pdata) #error 'names' attribute [37] must be the same length as the vector [8]
myNorm <- champ.norm(exprSet,method="PBC") #之前默认的是BMIQ,Alternatively: myNorm <- champ.norm()
QC.GUI(exprSet,pdata,arraytype="450K") # #再交互平台上看下图
#这行对吗?参数未变,但这个是看校正过的,理论上应该变化的?error 'names' attribute [37] must be the same length as the vector [8]
save(myNorm,file="myNorm.rda")
champ.SVD(beta=myNorm,pdata)
##Error in champ.SVD(beta = myNorm, pdata) : pd parameter in Data Frame or Matrix is necessary And must contain at least tow factors. If your pd is a list, please change its Format.
batchNorm=champ.runCombat(beta=myNorm,pdata) # If Batch detected, run champ.runCombat() here
##Error in champ.runCombat(beta = myNorm, pdata) : variablename parameter MUST contains variable in pd file
champ.SVD(exprSet,beta=batchNorm$beta)
##Error in which(is.na(beta)) : object 'batchNorm' not found
##下边的就没再运行
myDMP <- champ.DMP() #差异甲基化位点
#Error in champ.DMP() : pheno parameter is invalid. Please check the input, pheno MUST contain at least two phenotypes.
save(myDMP,file="myDMP.rda")
DMP.GUI()
myDMR <- champ.DMR() #差异甲基化区域
save(myDMR,file="myDMR.rda")
DMR.GUI()
myBlock <- champ.Block()
Block.GUI()
myGSEA <- champ.GSEA() #基因富集分析
save(myGSEA,file="myGSEA.rda")
myEpiMod <- champ.EpiMod() #网络分析
save(myEpiMod,file="myEpiMod.rda")
myCNA <- champ.CNA() #拷贝数变异,运行时间会很长
save(myCNA,file=myCNA)
急,急,其他的代码用的是生信技能树里分享的代码,非常感谢原作者
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