Questions tagged [statistics]
For statistical questions related to bioinformatics. If the nature of question is purely statistical, consider stats.stackexchange.com instead.
183
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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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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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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, ...
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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 ...
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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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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. ...
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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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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 ...
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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 ...
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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 (...
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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 (...
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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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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 ...
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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 ...
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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 ...
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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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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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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 ...
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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
...
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90
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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 ...
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172
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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.
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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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58
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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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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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76
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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
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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:
...
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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 ...
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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
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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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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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363
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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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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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568
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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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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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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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49
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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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215
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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....
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