Question: May I use NB.MClust package for RNASeq genes clustering instead of samples clustering?
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gravatar for J. Smith
13 months ago by
J. Smith50
J. Smith50 wrote:

Hi Friends,

I have find this paper https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2556-9 for RNASeq data clustering (CRAN package: NB.MClust: Negative Binomial Model-Based Clustering). They have used it for samples clustering in RNASeq data. Can it be also possible to clusters genes using this model based clustering?

nb.mclust rna-seq R • 572 views
ADD COMMENTlink modified 12 months ago by qian.li100000 • written 13 months ago by J. Smith50

Please explain what kind of data you have. What is genes?

ADD REPLYlink written 13 months ago by ATpoint38k

I want to use it to cluster RNASeq count data downloaded from TCGA. Genes refers to row names of TCGA count matrix here. I mean, I want to find groups of genes having similar counts across either normal conditions or separately in tumor conditions. I have already separated data for two conditions.

ADD REPLYlink modified 13 months ago • written 13 months ago by J. Smith50
0
gravatar for qian.li10000
12 months ago by
qian.li100000 wrote:

I'm the developer and maintainer of NB.MClust,and just saw your post.

Yes, you can use this package to clustering of genes based on RNA-Seq counts (normalized). However, the assumption in this model-based method requires genes not highly-correlated. I would suggest to filter out genes having strong correlation across all samples (normal+tumor) before using NB.MClust. This method does not require the input of phenotype or condition, so it is completely unsupervised.

I hope this is helpful for your research.

Qian

ADD COMMENTlink written 12 months ago by qian.li100000

Thanks a lot for your response.

ADD REPLYlink written 12 months ago by J. Smith50

Hi Qian, what normalization method would you suggest in this case?

ADD REPLYlink written 5 months ago by waiszecandylei0
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