Questions tagged [statistics]

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

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Truncated Chemical Names

Good Morning, I am currently researching treatment options for the Corona Virus from the CAS COVID-19 Antiviral Candidate Compounds Dataset available on the www.CAS.org. One issue we have run into is ...
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For gene enrichment analysis, what are the difference among ORA, globaltest, and GSVA?

I am still new to bioinformatics, but I would like to know more about the algorithms for gene enrichment analysis. I studied for ORA, ...
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Choosing Fisher's Exact or Binomial test for overrepresentation in PANTHER

The PANTHER website offers a tool to obtain the GO-based overrepresentation of a gene list (the analyzed list) versus a reference gene list. After entering both these lists, the tool asks to choose ...
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Predicting ATC codes at level 3 in python

I am trying to implement the algorithm implemented in this paper on Python. Basically it is a multi labeling algorithm to make out of sample prediction at level 1 of Anatomical Therapeutic Chemical (...
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Calculate proportion of survival and deaths from Life Table [migrated]

From the life table given, how do we calculate the proportion of newborns will survive to exact age 80 years but then die before exact age 85 years? I have tried using the formula (1 - l85/l0) but not ...
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1answer
33 views

Odds ratio and enrichment of SNPs in gene regions?

I did a QTL analysis with a panel of 7M SNPs, and want to analyze the enrichment of the significant qtl-SNPs in different genic regions (promoters, gene bodies, TFBS, etc.). A straightforward way to ...
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1answer
52 views

Compute the significance of the overlap between 2 or more gene sets

I was able to compute the significance of the overlap between 2 gene sets using the cdf function of scipy hypergeometric distribution. I wish to be able to perform the same calculation for more than 2 ...
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Retrieve ATC codes for New Clinical Trials

I have a STATA list of 4000 medicinals used in clinical trials and need to associate an ATC to them. I have scraped wikipedia and BBPharma website and found out some ATCs (missing and None included). ...
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24 views

B-factor analysis in nanobodies

I am doing my research on nanobodies. Currently, I am trying to do a comparison study of the flexibility of CDR loops using B-factor values. I would like to know if there is any statistical analysis ...
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Bootstrapping cell type identifications (scRNA-seq)

I have scRNA-seq data held in a SEURAT object, and cell-types were identified with SingleR (essentially a vector of strings - ...
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1answer
26 views

Bonferroni count = 1 in GO-Slim overrepresentation test (PANTHER) is it possible?

I encountered a problem while performing analysis using the PANTHER website. I run the statistical overrepresentation test for a genelist of 99 genes (GO-Slim BP, Binomial, Bonferroni) in February ...
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NCT search in PubMed via Entrez (python)

first time I post here so, please, be patient. So I am currently working with Entrez (Biopython) in order to retrieve the number of articles for a given disease/indication. My data provide both the ...
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1answer
28 views

How to generate Beta diversity boxplot from phyloseq object?

I am working with profiled metagenomic taxonomy abundance data. I want to generate beta diversity (bray-curtis) boxplot from a phyloseq object where two groups (control and test) will be shown. ...
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1answer
59 views

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG ...
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When should I plot rarefaction curve? after or before rarefying data? (Metagenomics shotgun data analysis )

I am analysing shotgun metagenomic data. I have profiled the sequences and now doing diversity analysis of the test and control samples. Can anyone tell me when should I plot the rarefaction curve? ...
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P-value correction when evaluating correlation between gene and miRNA expression

First of all I apologize without the question is very basic, I am taking my first steps in bioinformatics. Data information We are evaluating the correlation (using the Pearson, Kendall or Spearman ...
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Mathematics of “eXpress” paper

I am trying to follow the mathematics of the original paper of eXpress , specifically regarding equations (1) to (6) in the Methods section, in which the following explanation is given: The ...
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1answer
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What is the pvalue from anova(glm1, glm2, test = “Chisq”) telling me in R when the glms have a negative binomial distribution?

Having constructed two nested negbin glms in R, one has a dropped factor, We can do an anova with test = "Chisq" to ...
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Identifying substrates with enriched degradation potential from count data of enzymes able to degrade that substrate across all samples

How would I identify if I have enriched degradation of a certain substrate within a clade of bacteria with count data of enzyme capable of degrading a range of substrates? I have started of by ...
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39 views

Non-finite value supplied by optim in Hurdle model of enzyme count data

I have a dataset of enzymes counts that are grouped by substrate they degrade and am attempting to model if the origin of the genome in which the enzymes were found can predict the count for ...
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2answers
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What does aov(glm model) actually do in R?

What is happening when you use aov() on a glm model in R? Normal glm model sumamry(m1): ...
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2answers
42 views

Determining significance of a variable in a glm model

How would one determine the significance of a variable in a glm model? If I, for example, have a dataframe like seen below, how would I determine if the origin of the sample has a significant effect ...
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1answer
43 views

How do I set a neural network to loop multiple times and average the resulting values?

I have a script in R/RStudio which creates random datasets of binomial variables, feeds them through a neural network, and calculates their likelihood ratio statistic and deviance. I'd like the script ...
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1answer
22 views

Is outlier detection the right choice for determining if a value lies singificantly away from the mean in a population in gene frequency?

I have the following dataframe that is comprised of enzyme substrates as the variable and then the unique number of times enzymes capiable of degrading this substrates appeared in my genomes and then ...
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Regarding RNA seq data analysis and building coexpression network

I have some questions regarding RNA seq analysis if you can suggest anything it will help me a lot. I am currently normalizing RNA seq data for comparing genes expression within and between samples. ...
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1answer
35 views

Very low probability densities

I'm generating a density plot using the ggplot2 library: ...
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1answer
59 views

Inflated p-values in quantitative trait analysis

I am performing a quantitative trait association between the expression of one gene and ~400,000 methylation values. First, both variables are rank inverse normal transformed, adjusted for confounders ...
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Hypergeometic test for the overlap of two set of genomic intervals (e.g. from Chip-seq data)

Suppose I have done two Chip-seq experiments. Now after the bias correction step such as MACS2, I get two set of genomic intervals (or peaks, as what is usually called) that corresponds to each of the ...
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1answer
39 views

When should I apply a multiple comparison adjustment?

I am performing a RQL analysis ("http://www.esapubs.org/archive/ecol/E095/002/suppl-1.pdf"). This analysis meassures the relationship between different traits of three different matrix showing if ...
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2answers
27 views

Should you filter GWAS hits with high standard error?

I'm trying to figure out if I should be filtering out GWAS hits that have high standard error and I'm not quite sure what to do. It seems like it might not matter, because the standard error is used ...
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1answer
23 views

Arlequin files not able to converge beyond 2000 steps for some .arp files

When I use .arp files in arlequin to run mismatch distribution it says that can’t converge beyond 2000 steps and also no graphs are produced.can someone suggests what can I do to overcome this problem
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1answer
32 views

How to run Cox proportional Hazard model for each group in R?

My population is divided into 10 groups. I want to run the cox-proportional hazard model separately for each of these 10 groups so that in the end i can compare which groups has highest hazard ratio ...
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2answers
81 views

What is the difference between fixed effects and random effects in the context of Linear-mixed models?

The terms in LME i.e. fixed and random create confusion? What is the genesis that can distinguish between the two ?
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1answer
38 views

How to compute Shanon entropy

I want to analyze some viral sequences. I want to use shanon entropy as a measure to analyze the sequences. However I do not understand the concept of shannon entropy. Would anyone explain please how ...
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1answer
109 views

Comparing phylogenetic models with different datasets

I'm a linguist interested in phylogenetic tree inference using language data. I'm posting here because I'm using Bayesian phylogenetic methods in my work (probably using BEAST and/or RevBayes). For ...
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1answer
146 views

Prediction model for spread of coronavirus

A previous thread on Bioinformatics StackExchange citing an article by the Economist which references a cartoon of predictive outcomes by the CDC (Economist article on coronavirus) suggests a model in ...
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1answer
76 views

a package with randomization/permutation tests for genomic analyses

please would you let me know, is there a package in R/python/C that has implemented randomization/permutation tests for joint genomic analyses (an example of joint genomic analyses -- when jointly ...
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2answers
197 views

Economist article on coronavirus

I am wondering about an article in the Economist here: https://www.economist.com/briefing/2020/02/29/covid-19-is-now-in-50-countries-and-things-will-get-worse There is a graph there The explanation ...
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1answer
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How to deal with zeros in the denominator when calculating percent enrichment?

I have a data.frame with results from a CRISPR screen. I want to calculate the % enrichment of a variable of interest var from ...
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3answers
615 views

Calculating the mortality rate of a pandemic, e.g. coronavirus 2019-nCov?

When calculating how lethal a virus outbreak is, I've noticed that most sources use CONFIRMED_DEATHS/CONFIRMED_INFECTIONS However, given that there are only 2 ...
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2answers
44 views

How to exclude the repetition of gene-gene correlation calculation in python?

I am trying to make a paired matrix of gene-gene correlation. Considering that I have a huge matrix (13000 genes and 900 samples) and for some reasons I don't want to decrease the number of my genes, ...
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3answers
208 views

Is it possible to do this in R?

I have a big clinical data file with 96 columns like age, gender, BMI, etc I want to see which of these clinical characteristics respond to chemotherapy. Response to chemotherapy divides patients to ...
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2answers
49 views

Most scalable pseudotime ordering algorithm

What algorithms for linear Pseudotime trajectory construction (diffusion-based) are the most scalable to large datasets? I'm currently using Slingshot based on the recommendation in this manuscript: ...
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11 views

Quartert and Statistical Consistency

I found that triplet is statistically consistent, meaning, Given large amount data, most occurring Gene tree containing three taxa will likely be a true species tree I understand the proof. Is ...
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1answer
48 views

Use of Electronic Phenotype in EHR

May I know what's the use of Electronic Phenotyping using EHR data? I did refer this link but have few questions I understand that ...
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1answer
72 views

protein secondary structure matching/comparison scoring

I want to compare two secondary structures of aligned proteins. I do not know exactly how to do it well. Example: ...
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Recalculating fold change in microarray from a subset of samples

I have some bulk microarray data that I have pulled from online sources which describes the spatial distribution of transcription. The tissue in question has a few different subregions. I am ...
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44 views

Detect differentially expressing cells

after comments on my original post, I will ask my question again here I have data (RNA expression values, obtained with multi-channel in situ hybridization) collected from 1mio human cells. For each ...
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0answers
45 views

Trouble optimizing Five Parameter Logistic (5PL) Standard Curve for ELISA data using Python

I am writing a Python script to automate a 5PL Standard Curve for ELISA data, using an XLSX file template. I am using pandas dataframes to hold the 96 wells as ...
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1answer
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What is the state of the art for GWAS in terms of the statistical algorithm for either Case/control and Quantitative traits?

This question was also asked on Biostars I'm trying to understand what is the best algorithm for GWAS nowadays. I know we have many tools available like Plink and Hail, but currently, what is the ...