Questions tagged [clustering]

Clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense) to each other than to those in other groups (clusters).

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44 views

How are the values of prop.part() and prop.clades() calculated?

Consider the following dataset: ...
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57 views

Clustering issue about overlapping CD4, CD8, and Foxp3 genes in mouse tumor models

bioinformatics scientists. I hope your work goes smoothly well and be safe. I'm stuck in trouble at the step of clustering. Briefly, I downloaded fastq files from a published study (https://www.ncbi....
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32 views

vst() from DESeq2 vs voom() from limma

I have used both to transform my leukaemia RNA-Seq data for subsequent hierarchical clustering. The result is quite different. Some subtypes of leukaemia only form a cluster (or at least sit closer) ...
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1answer
121 views

sva for RNA-Seq data without known phenotype

I have been working on RNA-Seq data from two different cohorts, and they show very strong batch effect (~35% variance explained by 1st component in PCA). Since I am trying to do a class discovery from ...
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18 views

What is the best approach to classify a patient cohort by the expression (low, int, high) of a single gene of interest?

I am working with a dataset of nearly 100 patients. I performed Salmon quantification with genecodeV34 and imported the results with tximeta. I normalised the TPM salmon output with TPM (using edgeR, ...
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162 views

Understanding BuildClusterTree of Seurat

I am trying to understand how to use BuildClusterTree of Seurat to merge clusters. Being no informatics or statistical background, I am not understating how to use it. I am having the following ...
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100 views

Error using bseqsc

I will be very grateful for any hint on how to overcome the error. I wish to deconvolve my bulk RNA seq data obtained from the lungs of mice using single cell RNA seq data. For practice, I am ...
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54 views

How to write the subclusters in file?

I have constructed a gene co-expression network from RNA-seq data. The network file is in edge list format of memory around 1gb which was created by calculating Pearson correlation of each gene pairs ...
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119 views

GBS: clustering of PCoA axes with R package mclust to describe identity by missingness

I have a SNP dataset with 56 populations and 430 samples that was produced by GBS sequencing. I need to identify groups of samples that have similar patterns of genotype missingness, since there is ...
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243 views

How to create a dendrogram of clusters and reconstruct phylogenetic relationship

I'm working with a Daphnia data set looking at the 16s gene pulled from the BOLD database. So far I did a multiple sequence alignment and attempted to cluster and plot a dendrogram: ...
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50 views

case/control phenotype prediction - population stratification with R

I'm struggling these last days on a case/control phenotype prediction problem based on genotype (individual x SNPs with more than 10k individuals and approx 18k SNPs encoded as 0,1,2). Thanks to PCA ...
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23 views

which marker identifications method is recommended when single-nuclei RNA seq datasets are integrated across regions

I'm analyzing Sn-RNA seq datasets which include different brain regions and spinal cord in patients and normal controls. I would have different comparison within and between individuals. I've got a ...
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3answers
94 views

RNAseq biological replicates not clustering in PCA plots

I have RNAseq data from 4 samples with 3 biological replicates per sample. I am currently trying to do the differential expression analysis with DESeq2 but the biological replicates will not cluster ...
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89 views

Error in my RNAseq analysis

I was following the RNAseq analysis tutorial online(https://combine-australia.github.io/RNAseq-R/06-rnaseq-day1.html) but am not obtaining the same variance values for each row in the logcounts matrix....
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1answer
152 views

Clustering information saved in Seurat object

Seurat V2 had a option to find clustering information saved in object: PrintFindClustersParams(object = pbmc). How can I get the same clustering parameters from objects in Seurat3? Do I need to ...
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2answers
75 views

What kind of analysis is practically done on GSE data files?

I have a GSE data file in csv file format containing fields such as: ID, adj.P.Val, P.Value, t, B, logFC, Gene.symbol, Gene.title. In which adj.P.Val, P.Value, t, B, logFC fields being numeric. What ...
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21 views

Comparing between different set of clusters produced from the same network

I have a set of eight gene clusters which I obtained from clustering a network. However, I had to update the genes in the network at a later stage which lead to certain deletions (genes not present in ...
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47 views

Non-redundant set of indices for AAindex?

AAindex has 566 indices with real values for each of the 20 amino acids mostly from wetlab measurements. Many of these values are highly correlated, and thus do not make good features for ...
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32 views

Quality checking benchmarks for clustering

I'm currently working with several RNAseq datasets from the ENCODE database. My approach to assessing the quality of the data, i.e, reproducibility is by automating the assessment of expression ...
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132 views

How can I calculate and compare intra-cluster correlation for each GO term and pathway?

How can I calculate and compare intra-cluster correlation for each GO term and pathway? I want for all the genes, which belong to the same GO-term, calculate a similarity score. Each GO term can be ...