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Statistical test design question

I have condition as such mouse liver and spleen data. So in liver I have WT (Wild Type) and KO (knock out) as well as in spleen WT (Wild Type) and KO (knock out). I have to compare the parasite load ...
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49 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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30 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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2answers
37 views

residual Squared Coefficient of Variation (rCV²) vs Distance to Median (DM)

I am working with single cell RNA-seq data. I obtained the squared coefficient of variation (CV²) as a measure of gene expression variability: I want a metric to express gene expression noise that ...
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1answer
77 views

Significant gene set testing - limma

While I have used my title, it is more of a general statistics question regarding how these significance tests are carried out, these include decideTests and ...
2
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1answer
116 views

Understanding PCHeatmap outputs

I am currently trying to understand the purpose of these PCHeatmaps - part of the seurat package in R: All the online documentation I have searched for has only ...
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2answers
152 views

Extracting some part of a list

I have two normalized gene expression values (log2 of cpm) ...
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1answer
61 views

Extracting genes differentially expressed by Wilcox test

I have 2 cell types (NOF and CAF) cultures individually and also have been co-cultured with tumour like this picture. https://ibb.co/x8Ty1Wz If this is the log cpm of these 4 samples ...
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2answers
112 views

Genomics Statistics Problem

I have used a python script to identify target sequences in a DNA sequence file. There are two classes of sequence: coding and non-coding. I have identified 728 sequences of interest. 597 of these ...
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1answer
28 views

Continuing analysis based on a log-likelihood ratio? (Comparing methylation between two PoolSeq phenotypes)

I'm trying to get some pointers on where to start on the analysis of my dataset. First, some basic info: Background: We performed Nanopore sequencing of two poolseq samples called UU and DD referring ...
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0answers
29 views

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

Consider the following dataset: ...
2
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1answer
420 views

3D PCA group labelling

I would like to make a 3D PCA but not sure how to label group wise which i can do for 2D PCA ...
4
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1answer
49 views

Why are my Chi-squared test results different from those in a published table?

I recently read the paper “A novel long non-coding RNA linc-ZNF469-3 promotes lung metastasis through miR-574-5p-ZEB1 axis in triple negative breast cancer”. In this I see Table1 showing correlation ...
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1answer
31 views

What does it mean for an amino acid to match with itself 99% of the time in a PAM1 matrix?

In this video, the lecturer says: You see that phenylalanine is probably still phenylalanine because only one percent of amino acids have changed so roughly 99 percent of the time, phenylalanine is ...
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0answers
53 views

Block wise protein imputation

I am currently working on a dataset that contains 50 samples (10 samples * 5 blocks). The data is perfectly balanced between blocks, with equal treatment representation in each block. Each block ...
2
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1answer
39 views

How can the Autocovariances, autocorrelations, and autocorrelation coefficients be calculated from a Protein Amino Acid Sequence?

Given a normal protein sequence with the 20 standard amino acids, how can the 'Autocovariances', 'autocorrelations', and 'autocorrelation coefficients' of the sequence be calculated? What is meant by ...
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37 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 ...
5
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1answer
140 views

Should PCA be standardized for gene expression?

This is a theory/good practice question more than a technical one. If samples are being plotted on a PCA projection of gene expression data, I'm wondering whether it is standard (and if so, why) to ...
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1answer
64 views

A basic question about phylogenetic inference with Bayes-MCMC

I am new to the world world of Bayesian-MCMC inference and have been working my way through various texts. I am having some difficulty understanding how MCMC works. I understand that it is a way of ...
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1answer
64 views

To find p-value of compounds (pairwise)

I have next SNPs data.frame structure ...
2
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0answers
35 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. I also ...
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0answers
21 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/...
3
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1answer
142 views

Test to determine if two genes/exons share the same evolutionary histories?

In classic phylogenetic inference one is usually given various orthologue sequences of a given gene across various species. Those sequences are then multiple aligned and used to construct a ...
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0answers
59 views

Is there a way to do GWAS on phenotype data that is not normally distributed?

Is there a way to do GWAS on phenotype data that is not normally distributed? For example, if you were measuring a trait as a proportion, and the majority of the data consisted of 0.00. Or, perhaps ...
4
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1answer
79 views

LRT or LRT-like test on cyclical (Sleep) data

I have RNA-Seq data from 4 time points (3 hours awake, 9 hours awake, 3 hours asleep, 9 hours asleep). I'm interested in doing something similar to a LRT where genes are found to be significant if ...
6
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1answer
253 views

Intuitive explanation of GSVA analysis

I'm trying to understand the way the GSVA analysis is working behind the scenes.And I was wondering if there is any way to understand it more intuitively the whole process. So at first according to ...
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0answers
72 views

Normalize before using adonis?

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

Comparing two multi-fasta files of the same set of proteins with parser - to find and count mutations after treatment

My task is to count the mutations occurred in several proteins after a treatment. The sequences are all present in the two files in the same order. I opened both files with the FASTA parser (...
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0answers
44 views

Pathifier bioconductor package recommends to use technical noise for an argument. How to determine it?

I'm running the pathifier approach against C2 pathway curated database for a specific microarray dataset. As I was reading the documentation of the pathifier, in order to configure it properly for ...
8
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1answer
253 views

Comparison of gene set enrichment statistics

I am performing a gene set enrichment analysis to determine if particular gene sets are coherently up- or down-regulated. I have seen several statistics for computing a p-value of GSEA-style ...
8
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2answers
218 views

Comparing two genome annotations

I have one-dimentional array (human genome). Also I have two annotations for it, we can think about them as different peaks (it's nucleosome and secondary structures). How can we find correlation and/...
3
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1answer
74 views

Matlab scatter diagram

I have two columns of data, x and y, how can I make a ‘thermodynamic diagram’ with matlab? The z axis is the density value of dots, like below figure. The x-axis is angle, y-axis is distance. I want ...
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2answers
116 views

Can structural equation modeling be used in Bioinformatics?

I am a bioinformatics student and I was learning the basics of structural equation modeling (SEM) to help one of my friends. I was wondering, are there any applications of SEM in bioinformatics? Any ...
2
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1answer
95 views

Why do I obtain very strange results with DESeq2?

I am using DESeq2 to perform a differential expression analysis, but I obtained very strange results for some genes. For some genes, I have very high log2FoldChange with very low p-value as displayed ...
4
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1answer
56 views

Standard Cutoff for Moderated T-statistics

I'm looking at some microarray data. For the first time I've calculated a moderated T statistic from limma. Is there any standard practice for where to cut off that value? For log2 fold change I ...
3
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1answer
189 views

pvalue calculation of protein-protein network with permutation test

Note: this question has also been asked on Biostars I have performed a network recreation analysis based on the interactions of proteins from String db. I wanted to know if the interactions have ...
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0answers
32 views

What is the significance of the effect size on WOMAC scores for TKA?

https://www.medicaljournals.se/jrm/content/html/10.2340/16501977-2210 I understand the difference between statistical significance and effect size, but I am having trouble interpreting the data on ...
4
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1answer
397 views

Adjusting phenotypes by regressing out covariates

I'm trying to use the bfGWAS tool, which analyses GWAS data and integrates functional annotations to identify casual SNPs (paper and github). In the user manual, it states: We recommend first ...
7
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1answer
79 views

What will be an appropriate mathematical distribution for SNP data?

I found that several papers describe SNPs as a binomial distribution with the probability of "success" equals to minor allele frequency. However, in my experiments, when I generate SNP array ...
4
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2answers
845 views

What is the best distribution to model the FPKM values from normalized RNA-Seq data?

I know that the discrete raw counts from the RNA-Seq data are usually modeled by a negative binomial or a Poisson distribution, but what I am working on are the FPKM (Fragments Per Kilobase of ...
4
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0answers
91 views

Differences between TM and GDT-TS scores for structure comparison

What are the relative advantages / disadvantages of the TM (template modelling) and GDT (global distance test, total score) scores, used in protein structure prediction competitions, such as CASP? ...
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4answers
3k views

How to calculate p-values for fold changes?

I'm currently working with data from a Luminex multiplex assay. In this assay, the concentrations of 17 different analyte proteins were identified in 12 groups in triplicate. One of these 17 groups ...
2
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0answers
58 views

ngs time course experiment [duplicate]

I have a question regarding the RNA-Seq analysis. We have a time course data regarding a mouse model wt and mutant treated with a drug (10uM) and the taken down at different time points: 8 time ...
8
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1answer
288 views

When performing differential expression analysis, should genes with low read counts be removed before or after normalization?

I have RNA seq data which I've quantified using Kallisto. I'd like to use tximport to transform the read count data into input for EdgeR, following the R code supplied in the tximport documentation: ...
4
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2answers
563 views

How can I use Arlequin via the command line?

I've got a decent knowledge of programming (incl. bash scripting) but I fail to understand how Arlequin works. Could you please help me with a very simple reproducible example on how to use Arlequin ...
3
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1answer
36 views

How does Cellminer's “Cross-correlations of transcripts, drugs, and microRNAs” work

I have seen one of Cellminer tools. I am not sure how do they calculate the cross correlation of the genes, what does it actually mean? Based on what databases? For example if I take their example ...
5
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0answers
485 views

Difference between computational biology, bioinformatics and biostatistics [closed]

I find that in many contexts, the terms computational biology, bioinformatics and biostatistics are often treated as functionally equivalent, and yet for students selecting PhD programs and the like ...
4
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2answers
148 views

How to calculate statistical significance of sequence motifs

I would like to show that certain types of RBP motifs are enriched in RNA editing islands (i.e. clusters of RNA editing). However, I am unsure about how to think about sequence motifs with respect to ...
5
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1answer
766 views

How to select a power for a scale-free topology network

In a weighted gene co-expression network analysis (using WGCNA), the soft-threshold power is recommended as a noise filtering. It consists on raising the correlation to a certain number. To decide ...
9
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1answer
117 views

Expected allele frequency distribution of SNVs in real NGS data

I have a huge amount of ~20x human WGS samples, aligned, and all SNVs that were called with GATK under standard germline parameters set. What I need to do is to model SNVs Allele Frequency (AF) for ...

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