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Old 04-02-2015, 10:05 AM   #21
Gonza
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Location: Ithaca, NY

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Hi Blakeoft

I have used the suggestion you provided a while ago to get the names of the genes (not only XLOC) when using cummeRbund. I am now wondering if there is there a way to get the genes ID instead of their names? For example, instead of getting SHP2 I'd like to get AT2G42830. Thanks for your help.

#######

I have done this (as you suggested before):

cuff <- readCufflinks()

#Retrive significant gene IDs (XLOC) with a pre-specified alpha
diffGeneIDs <- getSig(cuff,level="genes",alpha=0.05)

#Use returned identifiers to create a CuffGeneSet object with all relevant info for given genes
diffGenes<-getGenes(cuff,diffGeneIDs)

#gene_short_name values (and corresponding XLOC_* values) can be retrieved from the CuffGeneSet by using:
names<-featureNames(diffGenes)
row.names(names)=names$tracking_id
diffGenesNames<-as.matrix(names)
diffGenesNames<-diffGenesNames[,-1]

# get the data for the significant genes
diffGenesData<-diffData(diffGenes)
row.names(diffGenesData)=diffGenesData$gene_id
diffGenesData<-diffGenesData[,-1]

# merge the two matrices by row names
diffGenesOutput<-merge(diffGenesNames,diffGenesData,by="row.names")
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Old 04-02-2015, 11:15 AM   #22
blakeoft
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Gonza,

There are several different types of gene identifiers. If you have a vector of gene names, you could take them to Ensembl's Biomart. There's also a Bioconductor package that can convert gene names as well. Be aware that mapping from one ID to another isn't always perfect. For example, you might get two Entrez IDs for the same gene symbol, but after looking up those Entrez IDs, you might find that only one of them is the right one for you. Unfortunately, I don't know how to fix that problem.
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Old 04-02-2015, 11:35 AM   #23
Gonza
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Thanks Blakeoft, will look into that !
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