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Questions tagged [statistics]

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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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1 vote
0 answers
30 views

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
0 answers
55 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. ...
liza's user avatar
  • 29
1 vote
1 answer
59 views

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 ...
n.osennij's user avatar
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2 votes
1 answer
56 views

Automate the def function in pandas for correlation

...
Riya's user avatar
  • 307
2 votes
0 answers
44 views

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
105 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
  • 351
2 votes
2 answers
153 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
70 views

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
89 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: ...
Gero's user avatar
  • 73
0 votes
1 answer
17 views

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
90 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
84 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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0 votes
0 answers
29 views

hypergeometric test in R

I have 15800 genes in a dataset, of which 5233 are differentially expressed, of which 1707 are upregulated. I have a second population of 17763 genes, I have selected a group of 119, of which 65 are ...
jonny's user avatar
  • 171
1 vote
0 answers
98 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
  • 141
0 votes
2 answers
66 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
0 votes
0 answers
29 views

MLPE in lmer (lme4 in R)

I am trying to conduct some landscape genetics analysis by testing association between landscape resistance matrices and pairwise genetic distances using linear mixed models. When I run lmer package, ...
RedPanda_Genetics's user avatar
3 votes
0 answers
34 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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1 vote
0 answers
237 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
34 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
  • 183
0 votes
1 answer
52 views

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
  • 75
1 vote
0 answers
20 views

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
282 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
  • 81
1 vote
2 answers
69 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
  • 1,462
1 vote
1 answer
55 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....
Lara's user avatar
  • 21
1 vote
1 answer
35 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
117 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
  • 1
4 votes
1 answer
136 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
159 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
44 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
90 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
101 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
70 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
171 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
1 vote
1 answer
50 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
1k 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 ...
monke's user avatar
  • 9
1 vote
0 answers
16 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
79 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
0 votes
1 answer
25 views

Where can I find a basic example for testing association between a phenotype and each of the variants of a chromosome?

I am a statistics student trying to find data suitable for a particular method. From what I have read so far, it is of interest to determine if variants within a chromosome are associated with a ...
variancekills's user avatar
1 vote
2 answers
81 views

What is the tP statistic from ANGSD?

We were looking for genetic diversity in the exon level of an MHC transcript and analysing the data under ANGSD (Analysis of next generation Sequencing Data) written in C++ We used ANGSD to calculate ...
mk894's user avatar
  • 85
1 vote
2 answers
28 views

P value recalculation from multiple analysis (Transcriptomics)

I've done a differential expression analysis with transcriptomic information (microarrays and RNAseq) from different datasets by applying for some of them t-test and for the rest Wald-test. I've got ...
Gero's user avatar
  • 73
0 votes
1 answer
383 views

How to create Beta Diversity distance boxplot

I'm trying to generate boxplot from Beta diversity boxplot between two conditions from a phyloseq object. I have a Morisita-horn distance generated by vegdist fonction : ...
Gaël.T's user avatar
  • 21
1 vote
0 answers
218 views

How to compare Log2 Fold Change values

I have 5 sets of Log2 Fold Change values pulled off DualSeqDB. Each of the 5 groups corresponds to a different microbial taxon. Within the 5 groups, there are many Log2 Fold Change values, each ...
pythonbeginner44's user avatar
0 votes
0 answers
32 views

How to decide between standardized mean difference (SMD) and log2fold change (log2FC) before doing meta-analysis?

I want to do meta-analysis of alpha diversity between test and control groups across 10 different populations. I want to see what is the summed effect (pool effect) of intervention between the two ...
DEEP's user avatar
  • 93
2 votes
0 answers
106 views

What are the best practices for comparing .seg copy number outputs from iChorCNA to VisCapCancer?

I have shallow whole genome sequence data that I used the tool iChorCNA to find the mean copy number segmentation per region. The tool produces a seg file and can be seen here: https://github.com/...
Dory Abelman's user avatar
3 votes
1 answer
43 views

Tajima-Nei Distance estimate with BioPerl

I have been trying to estimate Tajima-Nei distance for my data (link below). The output is s phylogenetics distance (pairwise) matrix which accommodates a detailed transition transversion and the ...
Mauri1313's user avatar
  • 185
0 votes
1 answer
20 views

How do you find differences when your metagenome sample size is small?

I received a matrix of genomics features (KEGG annotated metagenomes) abundance from 6 samples belonging to 2 groups. My collaborator is interested in finding differences between the two groups. The ...
Rob's user avatar
  • 3
0 votes
1 answer
60 views

How is the t-statistic value calculated in GEO2R or Bioconductor?

I was trying to calculate t-statistics using Python's scipy and numpy as np- ...
Vishal Kumar Sahu's user avatar
-1 votes
1 answer
107 views

Multiple box plot

I am using below code to plot multiple box plot but I am still struggling to understand how I can add whisker to box plot and how to change sample order like in this figure SampleType? ...
bioinfonext's user avatar