Questions tagged [statistics]

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Regarding canonical analysis of principal coordinates (CAP) for linking microbial data with elements

I used the below code to do CAP analysis to link microbial data with elements, but not sure how to do statistical analysis to show which element variation is responsible most for the difference in ...
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Confirmation about PERMANOVA and Variance partitioning (permutest)

Could you please help me to understand what is the difference between Permutational multivariate analysis of variance (PERMANOVA,adonis) and Variance partitioning (permutest). I understood that ...
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1answer
38 views

How to select specific lines and specific columns

Please I'm a beginner in using R and I work on database. I have a database that contain lot of columns and lines, like this for example ...
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1answer
44 views

How to calculate RNA copies in qPCR using R?

I have these Ct data from qPCR for a series of samples A-H, I want to quantify the RNA copies of my samples using R: ...
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27 views

Discrepany between AutoDock Vina and AutoDock Tools

I have been calculating the binding Affinity between a Ligand and a Protein using both AutoDock Vina and AutoDock tools but the binding affinity estimates obtained from the 2 molecular docking ...
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1answer
54 views

Comparing AUCs: Discrimination of same Control from different Test Group - paired or unpaired? miRNA

I want to compare two AUCs using a bootstraping method from pROC package (roc.test). I have done a classification using Logistic Regression and Serum miRNAs as prediction factors. The Controls are in ...
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1answer
36 views

Power law distribution alpha values

I did a Pearson co-expression analysis for generating networks for my tissue-specific (chondrocytes) RNA-seq data. I used R package poweRlaw to check for the power-law distribution. We got the ...
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1answer
57 views

error in random forest analysis

I am now struggling to do random forest analysis, I will be thankful if you could help with code for random forest analysis. I got samples from the root, soil, and leaf from two regions (bau & mau)...
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1answer
44 views

alpha diversity wilcox.test

I am trying to do Wilcox test to detect the significant difference in alpha diversity but it is showing an error? physeqN2 is a phyloseq object and Season is a metadata column. ...
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27 views

Truncated Chemical Names

[Note: this question has also been posted on KNIME] Good Morning, I am currently researching treatment options for the Corona Virus from the CAS COVID-19 Antiviral Candidate Compounds Dataset ...
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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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1answer
74 views

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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1answer
44 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
56 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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19 views

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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1answer
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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1answer
49 views

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
34 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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22 views

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
42 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
61 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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17 views

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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0answers
19 views

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
39 views

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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77 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
48 views

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
59 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
68 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
28 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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33 views

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
36 views

Very low probability densities

I'm generating a density plot using the ggplot2 library: ...
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1answer
61 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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2answers
113 views

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
29 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
35 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
59 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
82 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
39 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
114 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
158 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
87 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
202 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
72 views

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
650 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 ...