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For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.

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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 ...
Blaze9's user avatar
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2 votes
1 answer
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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 ...
Netanel Cohen's user avatar
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1 answer
17 views

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 ...
M.Bioinfo's user avatar
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3 votes
0 answers
29 views

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 ...
Johnson's user avatar
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2 votes
1 answer
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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 ...
K_081's user avatar
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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. ...
Subhash C. Davar's user avatar
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26 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 ...
bioinfonext's user avatar
1 vote
1 answer
96 views

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 ...
K_081's user avatar
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4 votes
2 answers
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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 ...
saplingmagic's user avatar
0 votes
1 answer
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 (...
bioinfonext'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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1 answer
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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
1 vote
0 answers
22 views

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
1 vote
0 answers
99 views

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
1 vote
1 answer
63 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 ...
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
1 vote
0 answers
38 views

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 vote
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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0 answers
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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 ...
Malik Saad's user avatar
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0 answers
22 views

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 Hamilton's user avatar
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0 answers
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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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1 vote
1 answer
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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
82 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
145 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
73 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
  • 121
2 votes
1 answer
58 views

Automate the def function in pandas for correlation

...
Riya's user avatar
  • 307
2 votes
0 answers
47 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
139 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
373 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
76 views

How to statistically test the strength and weakness of a correlated pair?

Subset of df before groupby looks like ...
Megha's user avatar
  • 395
2 votes
1 answer
266 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
18 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
101 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
  • 109
2 votes
1 answer
210 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
  • 21
1 vote
0 answers
153 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
  • 161
0 votes
2 answers
77 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
61 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
  • 71
1 vote
0 answers
347 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
49 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
57 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
522 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
124 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
  • 1,689
1 vote
1 answer
72 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
45 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
188 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
46 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
157 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
249 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
60 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