Questions tagged [statistics]

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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 (...
bioinfonext's user avatar
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How to create positive and negative Bar Graph

My Data: ...
Emy Alade's user avatar
1 vote
1 answer
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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 ...
Charles's user avatar
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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 (...
bioinfonext's user avatar
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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 ...
bioinfonext's user avatar
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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 ...
bioinfonext's user avatar
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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 ...
Laura's user avatar
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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 ...
TheNumber23's user avatar
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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 ...
dew's user avatar
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1 answer
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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 ...
Eliza R's user avatar
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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 ...
Saad Farooq's user avatar
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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 ...
Julius H.'s user avatar
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overrepresentation test, between transcriptome and candidates sequences obtained from the transcriptome

For an analysis of my data, I have a transcriptome and a list of sequences obtained from the transcriptome. I would like to perform a functional enrichment analysis. I have annotated both sets of data ...
se-tima's user avatar
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How to get enriched pathways in the data using continous statistic measure?

I was doing pathway enrichment analysis using the below code ...
Megha's user avatar
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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 ...
John Smith's user avatar
2 votes
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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. ...
liza's user avatar
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1 answer
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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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Automate the def function in pandas for correlation

...
Riya's user avatar
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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://...
R_Cres_01's user avatar
4 votes
1 answer
124 views

How to fix the Error in Kruskal Wallis rank sum test for comparing the guides in python? Also to check whether using the right test for my data?

df ...
Priya's user avatar
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2 votes
2 answers
274 views

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-...
M. Beausoleil's user avatar
2 votes
1 answer
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How to statistically test the strength and weakness of a correlated pair?

Subset of df before groupby looks like ...
Megha's user avatar
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2 votes
1 answer
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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: ...
Gero's user avatar
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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 ...
Angus Campbell's user avatar
2 votes
1 answer
97 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 ...
CorteZero's user avatar
2 votes
1 answer
153 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 ...
Kelly's user avatar
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137 views

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 ...
Marco's user avatar
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2 answers
72 views

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 ...
user3377241's user avatar
3 votes
0 answers
43 views

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 ...
albertr's user avatar
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319 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 ...
Farinelli's user avatar
2 votes
1 answer
45 views

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 ...
gaspanic's user avatar
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1 answer
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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 ...
Mendel's user avatar
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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 ...
beginbio's user avatar
1 vote
1 answer
420 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. ...
YP CHEN's user avatar
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1 vote
2 answers
100 views

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 ...
user438383's user avatar
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1 vote
1 answer
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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....
Lara's user avatar
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1 vote
1 answer
42 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 ...
bioinfonext's user avatar
0 votes
0 answers
163 views

How to do enrichment analysis with scipy.stats.hypergeom.sf function

I want to do pathway enrichment analysis in python using scipy.stats.hypergeom.sf function to select pathways that are significantly enriched in at least one tissue....
Riya's user avatar
  • 307
0 votes
1 answer
45 views

IBM SPSS- 2-years survival of cohort

Over the past few months I have been retrospectively analyzing patient files for my master's thesis in medicine. As the median overall survival of my cohort is low, I have decided that I want to ...
Leon's user avatar
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4 votes
1 answer
151 views

LD Score Regression Derivation hard to follow

I am trying to understand the derivations from Sullivan et al. (2015) in the Supplementary Material. There, it is mentioned in the first page that the least squares estimate of the j-th SNP effect, ...
Vasilis Lemonidis's user avatar
2 votes
2 answers
226 views

Comparing differential expression across samples - is batch effect correction needed?

I have a bulk RNA-seq dataset made up of control and treatment conditions for a range of cell lines. This dataset was generated in two batches, such that the cell lines are split between batches but ...
Bobbybobbobbo's user avatar
0 votes
2 answers
55 views

How Does Cox Proportional Hazard Model Describe Interaction between Covariates

I have read STDHA and the documentation for the coxph() function in R. I understand that the cox PH model explores how different covariates simultaneously impact survival. Based on the Lung data ...
dunkindonts's user avatar
2 votes
1 answer
133 views

What statistics can I use on qPCR data composed of several runs if all normality tests fail on the dataset?

I have >100 qPCR experiments that I'd like to analyze together, each containing the same set of genes (10 genes of interest and 2 reference genes). I have four different samples (untreated & 3 ...
vhio's user avatar
  • 21
0 votes
0 answers
116 views

Linking UK biobank patient IDs with their corresponding genetic data

I am analyzing ukbb data and I have patient IDs for both cases and controls. Now I want the genetic data of all patients based on their IDs. I am trying to test with chromosome 5 as I have both bgen ...
Muhammad's user avatar
0 votes
1 answer
96 views

Understanding the different designs in DESeq2

I am using DEseq2 and trying to understand the results obtained using different models. I have a data design with 2 genotypes and 2 time points. ...
yathrakaaran's user avatar
5 votes
1 answer
213 views

UPGMA computation

The unweighted pair group method with arithmetic mean (UPGMA) is a hierarchical clustering method, for example used in phylogeny. In a phylogenetic tree it would result in a global molecular clock ...
xxxcompbioxxx's user avatar
2 votes
1 answer
62 views

Statistical or performance test for genomic intervals between 2 samples

Is there an appropriate statistical or performance test to perform when I want to compare genomic intervals between 2 samples. Sample A is the the benchmark of comparing the intervals and sample B is ...
aBiologist's user avatar
-1 votes
1 answer
2k views

Adjusted P-value from DESeq2

What does the padj really mean? I believe it's a BH method, where it attempts to quantify the likelihood of a "false positive" but I am not sure. Also, what does it mean if the resulting ...
CodeMonke's user avatar
1 vote
0 answers
22 views

General Question: Statistical Alternatives to Oncoprint

I am a computational genomics student who has recently joined a research lab as an RA. We often work with oncoprints (comuts/heatmaps), and we visualize molecular signatures by reorganizing the comut. ...
dunkindonts's user avatar
0 votes
2 answers
86 views

Question about the practical relevance of chromosome position and p-value

Article of interest: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023908/#SD1 Referring to Figure 2b of that article, if I understand correctly, the x-axis refers to the position of each variant in a ...
variancekills's user avatar