How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
2
0
Entering edit mode
llkxiaolan • 0
@llkxiaolan-13767
Last seen 4.1 years ago

I'm analyzing a bunch of data from the Affymetrix Human Genome U133 Plus 2 Array platform, but I'm not going to replace the probe ID with the gene ID, and I've looked at some information, but the problem hasn't been solved. (My English is not very good, I hope you can understand the problem I described, thank you very much )

library(oligo)
celFiles <- list.celfiles()
affyRaw <- read.celfiles(celFiles)

library(pd.hg.u133.plus.2)

eset <- rma(affyRaw)

library(limma)

design <- model.matrix(~ 0+factor(c(1,1,1,2,2,2)))
colnames(design) <- c("group1", "group2")
contrast.matrix <- makeContrasts(contrasts="group2-group1",levels=design)
design
fit <- lmFit(eset, design)
fit1<- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(fit1)

dif<-topTable(fit2,coef="group2-group1",n=nrow(fit2),lfc=log2(2))
dif<-dif[dif[,"adj.P.Val"]<0.05,]
head(dif)

How do I transform the probe ID into the gene ID? 

oligo annotate • 3.6k views
ADD COMMENT
0
Entering edit mode
Guido Hooiveld ★ 3.2k
@guido-hooiveld-2020
Last seen 23 hours ago
Wageningen University, Wageningen, the …

This works exactly the same as for the mogene 2.0 ST arrays, which you asked before A: How to annotate the [MoGene-2_0-st] Affymetrix Mouse Gene 2.0 ST Array chip ....

1) Guideline: prefer a ChipDb annotation package over a PdInfo package.

2) Check the Bioconductor annotationDb webpage here for the platform you are using; you will find this page: Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2).

3) Use biocLite() to install the package.

4) Use the function annotateEset() from the the package affycoretools to annotate your normalized data.

ADD COMMENT
0
Entering edit mode

First of all, thank you very much for your reply. In fact, I want to say, the two methods I have tried, but did not do it, the following is the wrong tips 

This is the first method,using the PdInfo package

library(oligo)
celFiles <- list.celfiles()
affyRaw <- read.celfiles(celFiles)

library(pd.hg.u133.plus.2)

eset <- rma(affyRaw)

library(affycoretools)

eset<- annotateEset(eset, pd.hg.u133.plus.2)

错误: There is no annotation object provided with the x package

Here are second ways, using the ChipDb package

library(hgu133plus2.db)
eset<- annotateEset(eset,hgu133plus2.db)

And then there was a hint :select()' returned 1:many mapping between keys and columns

And then I didn't know what to do 

ADD REPLY
0
Entering edit mode

That's not a hint. It's a message that some of the probesets map to more than one thing. By default you get just the first thing, although there are arguments that you can use to get all the mappings. But you claim it doesn't work without apparently even looking at the output. You should probably make sure it didn't work before you come here to make claims.

ADD REPLY
0
Entering edit mode
llkxiaolan • 0
@llkxiaolan-13767
Last seen 4.1 years ago

First of all, thank you very much for your reply. In fact, I want to say, the two methods I have tried, but did not do it, the following is the wrong tips 

This is the first method,using the PdInfo package

library(oligo)
celFiles <- list.celfiles()
affyRaw <- read.celfiles(celFiles)

library(pd.hg.u133.plus.2)

eset <- rma(affyRaw)

library(affycoretools)

eset<- annotateEset(eset, pd.hg.u133.plus.2)

错误: There is no annotation object provided with the x package

Here are second ways, using the ChipDb package

library(hgu133plus2.db)
eset<- annotateEset(eset,hgu133plus2.db)

And then there was a hint :select()' returned 1:many mapping between keys and columns

And then I didn't know what to do 

 

 

ADD COMMENT

Login before adding your answer.

Traffic: 186 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6