Questions tagged [statistics]

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36 questions with no upvoted or accepted answers
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1answer
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Find covariation of different DNA-binding protein binding between two conditions

I have ChIP-seq data of RNAPII and two other factors which we think follow RNAPII during transcription in two different conditions, and I'd like to show that the genes that lose RNAPII also lose the ...
4
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1answer
133 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 ...
4
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1answer
67 views

What is the correct way of dealing with the analysis of data from flow cytometry?

I would like to detect a change in expression of a molecule present on a cell type by flow cytometry. Assuming I am able to detect, using an antibody, a signal that represents the amount of the ...
4
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0answers
56 views

Correcting for noise in RT-qPCR gene expression data

I have a training set of RT-qPCR gene expression data (not run in triplicate) for a batch of samples with two phenotypes $A$ and $B$ on which I've trained a "logistic regression classifier". ...
3
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0answers
57 views

How are the values of prop.part() and prop.clades() calculated?

Consider the following dataset: ...
2
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0answers
26 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/...
2
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0answers
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 ...
2
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0answers
59 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 ...
2
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1answer
104 views

How to interpret Mendelian randomization results?

I did Mendelian randomization using this software: https://cran.r-project.org/web/packages/MendelianRandomization/vignettes/Vignette_MR.pdf ...
2
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0answers
53 views

Number of reactions per metabolic pathway

What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database such as Kegg, MetaCyc,Reactome is more helpful/reliable ...
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0answers
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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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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0answers
77 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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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 ...
1
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1answer
55 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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2answers
154 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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0answers
45 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 ...
1
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0answers
168 views

Should I use log2-CPM values (voom-limma) as input for my model?

We have created a model to integrate several OMICs data, but we realized that the maximum TPM values of RNA-Seq data were so big that had unexpected effects on our results. We hypothesized that this ...
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0answers
51 views

What are the mathematical assumptions and algorithmic procedure behind MACS2?

I wonder if there's some mathematical details that outline what the algorithms does.
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0answers
22 views

Any input as to what to study in order to work into genetic engineering from math background?

Any input as to what to study in order to work into genetic engineering from math background? I have troubles understanding what the "interface" would be between mathematicians and biologists/...
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0answers
143 views

Normalize before using adonis?

I'm using adonis, an implementation of MANOVA in R (vegan package) to understand how continuous (temperature, pH) and ...
1
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1answer
328 views

Biplot scores from canonical correspondence analysis

I'm using the R package vegan to perform canonical correspondence analysis (CCA). As input we have two matrices, one being (sites)x(species) and the other being (sites)x(conditions). Sample data (...
0
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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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0answers
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 ...
0
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0answers
133 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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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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0answers
34 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 ...
0
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0answers
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 ...
0
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0answers
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 ...
0
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1answer
81 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. ...
0
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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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46 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. ...
0
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1answer
57 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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122 views

length of 'dimnames' [1686] must match that of 'dims' [3]

Please if anyone has experience with the use of the BSEQ-SC package for the deconvolution of bulk RNA sequencing data with single cell RNA sequencing data I will be very grateful for your suggestion. ...
0
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0answers
64 views

Which statistical test to use for comparing two groups?

I have data for 396 transcriptional factors (TF), where I have calculated the number of Transcriptional targets for each transcriptional factor present between the two groups: Group-I(G-I): where co-...
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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? ...