Clustering for count data based on poisson or negative-binomial model using MBCluster.Seq
GeneID<-countTable[,1]
Count=countTable[,-1];
Normalizer=rep(1,ncol(Count))
dim(countTable)
[1] 36536 5
Treatment=c("SRX017796","SRX017797","SRX017795","SRX017794")
n=20
mydata=RNASeq.Data(Count,Normalize=NULL,Treatment,t(GeneID))
c0=KmeansPlus.RNASeq(mydata,nK=n)$centers
cls=Cluster.RNASeq(data=mydata,model="nbinom",centers=c0,method="E+ M")$cluster
[1] "--->>>> iteration stops after 0 steps"
tr=Hybrid.Tree(data=mydata,cluste=cls,model="nbinom")
[1] "level 1"
Error in pairs[i, 1] : subscript out of bounds
This is my code and the last error , i need help im stuck with that.Any suggestion and help would be highly appreciated
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ayeshabhatt459 •
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1769mkc
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1769mkc
2 answers
For negative binomial model, there is another R package for RNA-Seq clustering: NB.Mclust. It applies to unsupervised clustering without biological group.
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qian.li10000 •
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