# Questions tagged [statistics]

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### Pathway enrichment analysis - minimum amount of proteins?

I have 6 proteins significantly associated with an outcome and have done a pathway enrichment analysis (PEA) with them (in both Enrichr and R with the same outcome). However, I wonder if that is too ...
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### DNA sequences of random base pairs

I'm a computer scientist studying measures of complexity across various data domains. One of these is DNA sequences, about which I have only basic knowledge. I believe that masking out so-called 'low-...
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### short Read/percentage threshold for bacterium presence in metagenome

I have ~100 paired end short read human gut metagenome samples that I classified using Kraken2. Now I want to know if a specific bacterium is in any of those samples. As far as I've searched people ...
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1 vote
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### Normalization in Sequence Analysis Research

I am currently engaged in a research project that involves DNA sequence analysis, utilizing nanopore and KMA alignment software (k-mer alignment). As I delve deeper into my research, I am faced with a ...
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1 vote
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### time*treatment series with repeated (i.e: NOT independent) sampling of replicates

I am performing the analysis of cell cultures in suspension, untreated(U) and treatment A and B, at t0, t1 and t2, 4 replicates per treatment. The experiment started with 12 cultures, 4U, 4A and 4B, ...
1 vote
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### Is this the correct method for determining Power at a given alpha, VAF, and coverage threshold?

I'm trying to calculate power at a given VAF, target coverage, and alpha. For example, what would my power be for a 100x coverage site, detecting VAF of 0.10 with an alpha of 0.05. This is what I came ...
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### permutation test in edgeR

I have a simple RNA-seq experiment with treatment and control, each with 3 biological repeats. I run my data through edgeR and obtained differentially expressed genes (DEGs). Due to the low sample ...
1 vote
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### SNP Signatures with Limited WGS Data:

On 80 WGS samples, I'm dissecting SNP signatures linked to milk production in a scarcely studied animal. Post-variant calling and QC association analysis have been tricky. I'm here to tap into our ...
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### How to do post hoc comparisons after a repeated measures ANOVA in R

I have a data set of several samples with their expression of proteins, in response to four different doses of a drug and two genotypes. I have been able to generate the two-way ANOVA using ezANOVA ...
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### Calculating Fisher's exact test for COG categories

This is a continuation of the following question - Fisher's exact test for COG categories in pan, core genome analysis Also, the dataset - How do I perform a Fisher's exact test on this data to ...
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1 vote
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### In medical and public health care, should we make use of "clinical" signficance testing (non-parametric tests) or parametric tests of significance?" [closed]

In certain cases, traditional significance test may not be able to identify that effect of a treatment or a drug is significant. However,clinical significance test may suggest a significant effect. ...
48 views

### limma linear model with interaction

I want to run some epigenome wide association studies based on city and pollutant type, could you please suggest if I can get DNA methylation sites (CpG) association based on pollutant type for each ...
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1 vote
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### Fisher's exact test for COG categories in pan, core genome analysis

I have come across several papers that do a Fisher's exact test to show over represented genes in COG categories specifically in a pan-core-accessory-species specific genome analysis. The test is done ...
• 149
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### probability of finding a 5 amino acids in a row within a proteome

How to calculate the probability of finding two proteins that share a 5 amino acid long motif from a proteome of around 1067 proteins that have an average length of 65 residues. The probability of a ...
104 views

### Statistical approach to link DNA methylation with toxic element exposure and health outcome

I would be thankful to you if you can help with the statistical approach for case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
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1 vote
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### Intepreting and applying ordinal logistic regression coefficients to calculate probabilities?

Can someone help hint me how I can interpret ordinal logistic regression coefficients and how I can use the .L, .Q and .C terms to calculate probabilities? I am analysing a dataset, where people ...
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### Mendelian randomization

I would be thankful to you if you can help with how I can use MR from my case-control study to link DNA methylation (epic array) with toxic element exposure (arsenic) and health outcome (...
• 393
1 vote
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### DNA methylation mediator analysis for environmental exposure and health outcome

We measured blood DNA methylation using epic array in 100 no-diabetic and 100 type 1 diatbetic patients matched for age, sex and smoking and also measured arsenic exposure using ICP-MS. Could you ...
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1 vote
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### Q-Q plots and the genomic inflation factor (k)

I have done the limma association analysis using below model design but not sure how to evaluate Potential systematic biases using Q-Q plots and the genomic inflation factor (k). Could you please ...
• 393
1 vote
66 views

### Using average of sequence similarities when delimiting genera - how to deal with outliers?

Sometimes I am trying to see where a (bacterial) genus ends and where another one begins based on 16S rRNA phylogenies. Of course, the length and support of the branch matter a lot, but this question ...
• 1,017
1 vote
25 views

### Metrics to use to estimate variant library evenness, uniformity, or bias

I have a 15k library of variants (OTUs) from a genome region. I want to compare the evenness of this library and understand of the library bias. I tried different methods to calculate evenness or ...
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1 vote
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### enrichment of DE genes within wide regions not pathways, hypergeometric test or GSEA?

I haven't found any relevant posts, so here is my question (it's more a question on statistics I believe): I have the deseq2 output of DE genes( around 25000 genes) , and among them 1000 are ...
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1 vote
56 views

### Gene Set Comparison Without Expression Data

I have been looking all over the web to find some answers to my problem but unfortunately, I was unsuccessful. I wish to determine whether an a priori defined set of genes in my case genes associated ...
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1 vote
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### What statistical analysis should I perform on DNA variants from unequal number of case (34) and control (11) samples?

I have performed NGS on 34 patient samples and 11 controls. Now I have variants from both groups but there is obvious difference in number of variants. How can I compare variants of both groups ...
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### The mathematics of kinship (degrees and distributions of relatedness on individual and group levels)

I have been thinking about to what extent a biological entity’s characteristics can be decomposed into discrete sections of the genome that are parsed and mapped one-to-one to a physical structure. It ...
1 vote
31 views

### How to get enriched pathways in the data using continous statistic measure?

I was doing pathway enrichment analysis using the below code ...
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1 vote
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### Heritability estimate in LD Score Regression (LDSC)

I am trying to replicate the heritability estimates based on the insomnia GWAS summary statistics using LDSC. However, I have encountered a problem as my estimates seem to be only about half of the ...
172 views

### Simes method in R

I have data that looks like this: 3 column SNPs their gene based on Annovar and a p-value for every SNP. What I would like is to aggregate the p values for every gene. ...
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1 vote
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### GLM for multinomial using r - results of genotyping

I have next data: age - how old is person, e.g. 17 or 25 bmi - body mass index, e.g. 18.25 or 29.35 rsXXX - results of genotyping in rs(point), e.g. rs10852521: C/C, C/T and T/T I devide all data ...
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### Using Multi-Dimensional Scaling (MDS) to produce a vector in order to account for patient bias when constructing DGE lists from RNA-seq datasets in R?

I am currently working on my PhD and as part of my thesis, I intend to analyse gene expression within multiple sclerosis (MS) lesions by looking at RNA-seq datasets on Gene Expression Omnibus (https://...
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df ...
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### How to z-transform Fst and -log(p) values for genome wide selection scan?

I saw in the literature a lot genome wide scans showing $F_{ST}$ values in a 'z-transformed' format which seems to be bounded between 0 to infinity. Examples are found easily searching for 'genome-...
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### How to statistically test the strength and weakness of a correlated pair?

Subset of df before groupby looks like ...
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342 views

### Genomic inflation factor distribution (lambda)

Considering that the p-value of a chi statistic(df=1) is uniform, the expected genomic inflation factor is λ=1. I show its calculation in R with the next chunk of code: ...
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### Understanding regularization step in Meta-cell pre processing

I'm reading through this paper: Baran, Y., Bercovich, A., Sebe-Pedros, A., Lubling, Y., Giladi, A., Chomsky, E., ... & Tanay, A. (2019). MetaCell: analysis of single-cell RNA-seq data using K-nn ...
105 views

### Multivariate analysis of cell culture bioprocess

I am seeking statistical support for the following bacterial growth time series. In the lab, we have cell cultures growing in bioreactors. Every day we measure the concentration in mmol-1 of a set of ...
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240 views

### Non-parametric, background-based tests on proteomics data from Proteome Discoverer v2.5?

I am new to proteomics analysis, so apologies if my question is silly! For context, I am working with proteome samples from the postmortem human brain for a case-control study. Our lab generally ...
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1 vote
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### Clustering individuals by gene presence/absence

I have a binary matrix with individuals as row names, and gene name as column name. So, if the gene is present in an individual, we have 1, otherwise 0. I would like to cluster individuals based on ...
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### Regarding chi square?

I need some suggestions regarding an analysis. I might be wrong as I have no stats background. I have list of exon with differential usage across samples. I can find lots of denovo mutations from both ...
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### How to select the best ligands in a virtual screening matrix

I have the results of a virtual screening experiment using docking simulations with Autodock Vina. The result is a matrix of 7 (proteins) by 28000 (ligands) with the calculated binding energies for ...
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1 vote
363 views

### How to calculate distance matrix from fasta?

I’d like to perform the following, but I am having difficulty. I want to convert amino acid sequences in multifasta files into matrices (or vectors) with Euclidean distance and Pearson correlation ...
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### Statistical significance of pairwise protein sequence alignment

I have identified a conserved region in a protein I'm studying, by doing multiple sequence alignments against a dozen of its orthologs. I've then found that this region also aligns relatively well ...
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### statistical test and visualization of genes present in an experiment

I have a list of genes (n = 120) that are involved in breast cancer. And I have a list of differentially expressed genes (n = 70) that are present in the breast cancer gene list. My question is: Are ...
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1 vote
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### Calculating the effect of differences between two groups of nucleotide sequences at every position

I'm investigating two different groups of short nucleotide sequences. The behaviour of a certain DNA-binding protein is likely influenced by common differences between these two groups leading high or ...
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1 vote
568 views

### Why all values become 1 after dcast?

I am reshaping my dataframe as follows. I want to set the Wavelength column as the column names with the code as follows. ...
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1 vote
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### Why is the p-value significance threshold for HLA association tests $5*10^{-8}$? [closed]

Typically, a p-value of $p<=5*10^{-8}$ is used for genome-wide association testing, as there are roughly $1/p$ independent LD blocks in the human genome, so it correct for multiple testing across ...
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1 vote
77 views

### What is the best way to perform batch ajustment between two experiments?

I have duplicate drug efficacy experiments performed six months apart. I would like to know what is the right way to perform statistical analysis to understand fold changes after treatment with a drug....
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1 vote
49 views

### Association analysis for methylation beta value and phenotypes in R

I am trying to learn how to do association analysis of methylation array data with numerical trait like body weight, eGFR. As I have seen some of the publications, methylation data association with ...
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