Questions tagged [statistics]

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19 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. ...
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1answer
32 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 ...
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1answer
92 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 ...
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13 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. ...
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62 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 ...
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1answer
20 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 ...
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13 views

What is the tP statistic from ANGSD?

We were looking for genetic diversity in the exon level of an MHC transcript. We used ANGSD to calculate Thetas, Tajima and Neutrality tests and one of the thetas was a pairwise theta, however I am ...
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2answers
17 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 ...
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0answers
121 views

How to group rarefaction curves by metadata

I'm trying to generate a rarefaction curve plot from a phyloseq object. I'm using the function ggrare using rarecurve function from the vegan package: The function rarecurve allow the ploting of all ...
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1answer
36 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 : ...
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0answers
11 views

How to find the minimal size effect in GWAS study

I'm new to bioinformatics and I have an assigment which I have to find the minimal size effect with power=0.9 in GWAS research paper of my choosing. I don't know how I'm supposed to calculate this ...
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33 views

co-occurrence analysis and visualization for amplicon microbial data

I am trying to learn co-occurrence analysis for microbial data. I got relative abundance at the genera level for 50 genera in 19 samples. I understand that for network analysis first I need to do ...
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0answers
52 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 ...
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24 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 ...
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25 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/...
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17 views

Tajima-Nei Distance estimate with BioPerl

I have been trying to estimate Tajima-Nei distance for my data (link below). I´m following this protocol from BioPerl: https://metacpan.org/pod/Bio::Align::DNAStatistics I have 314 sequences in a ...
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1answer
17 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 ...
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1answer
12 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- ...
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1answer
92 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? ...
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40 views

How to read E-value annotation on NCBI BLAST?

i am a bit confused how to read the current E value annotation on NCBI BLAST results. I looked into the matter but could not find an factual answer . What i understood so far: E -values are the ...
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1answer
151 views

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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1answer
183 views

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
79 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
63 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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0answers
76 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
64 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
107 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
61 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
80 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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0answers
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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1answer
168 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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1answer
57 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
67 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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1answer
37 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
53 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
54 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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1answer
133 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. ...
1
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1answer
63 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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1answer
31 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 ...
2
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1answer
42 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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2answers
67 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
150 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 ...
1
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1answer
175 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
32 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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0answers
45 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
38 views

Very low probability densities

I'm generating a density plot using the ggplot2 library: ...
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1answer
89 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
258 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
40 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
44 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 ...