Question: How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
0
gravatar for llkxiaolan
23 months ago by
llkxiaolan0
llkxiaolan0 wrote:

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? 

annotate oligo • 1.6k views
ADD COMMENTlink modified 23 months ago • written 23 months ago by llkxiaolan0
Answer: How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
0
gravatar for Guido Hooiveld
23 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

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 COMMENTlink written 23 months ago by Guido Hooiveld2.5k

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 REPLYlink written 23 months ago by llkxiaolan0

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 REPLYlink written 23 months ago by James W. MacDonald51k
Answer: How to annotate the Affymetrix Human Genome U133 Plus 2.0 Array chip
0
gravatar for llkxiaolan
23 months ago by
llkxiaolan0
llkxiaolan0 wrote:

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 COMMENTlink written 23 months ago by llkxiaolan0
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