Questions tagged [bioinformatics]

The discipline at the crossroads of computing and the biological sciences, which involves organizing, maintaining, and analyzing data from such fields as molecular biology, genetics, and genomics

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11 views

Is it viable to use ML models sequentially in a pipeline?

I have a machine learning model that predicts whether a gene is likely to cause a disease (the prediction is a probability score for a gene between 0 to 1, so a 1 score gene causes the disease and a 0 ...
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195 views

Is there a way to measure the degree of similarity between two columns?

I have a dataset of a list of genes with predicted scores (of likelihood to cause disease) from 2 different machine learning classifiers: ...
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10 views

DNA Nanoarray cluster plot

I don't understand picture B, it`s an Cluster plot of normalized intensities from a high-density test array with 700nm center-to-center spot distance. This array has 3,4 fold more DNA spots per image ...
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1answer
85 views

Is it possible to normalize features by one specific feature?

I have a dataset of genes with features that describe the genes at different scales (epigenetic, protein, cell, drug data etc. all numeric data). I use this dataset in supervised ML with a xgboost ...
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1answer
28 views

Is it possible to use a feature as a mediator of other features in machine learning?

I have a dataset of genes with features that describe the genes at different scales (epigenetic, protein, cell, drug data etc. all numeric data). I use this dataset in supervised ML with a xgboost ...
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2answers
24 views

Differential gene expression using R

I am working on RNA Seq data analysis to get differential gene expression between 2 conditions. I am using ballgown package on R, and successfully loaded the data into R. However, I do have these ...
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7 views

Differential correlation between two condition across multiple time-steps

I have an experiment which is performed across 4 time-steps, 2h, 6h, 10h and 24h. At each time step, I have 6 samples across 2 conditions, 3 in each condition. For each sample at each time-step, ...
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1answer
19 views

Association between groups of features and outcome variable

I am working with a high-dimensional dataset (e.g., ~150 features) and possible confounders (e.g., ~10 features to control). The goal is to identify association with an outcome variable that is ...
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70 views

Statistically comparing two scatter plots in R

I have 2 different data sets (gene expression) where the same samples have been run on different platforms and the data has undergone different types of normalization. I have performed umap ...
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17 views

FDR control on many t-tests performed on different sample size

I'm a PhD student working in bioinformatics, on genome sequencing data. My knowledge comes to its limits here on hypothesis testing and FDR-control/multiple-comparisons. Any help would be truly ...
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1answer
35 views

How to do ANOVA analysis for therapeutic biomarker screening for drug sensitivity

I am new to Bioinformatics. The graph below (from GDSC database) is to find therapeutic biomarker for drug sensitivity. I wonder how to do this kind of ANOVA analysis on my own so as to make this kind ...
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23 views

residual plot interpretation

I am currently analyzing biological data where the dependent variable is a logarithmically transformed gene expression normalized counts data. So originally gene expression had 0 counts but then when ...
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20 views

How do I record randomly assigned data succinctly in a table

Please forgive me if I am posting this in the wrong forum. Here is the context of my question: I am conducting a drug trial, of sorts. I have 7-8 potential candidates for the treatment. Between ...
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1answer
23 views

How to choose a relevant threshold for HWE

I'm a beginner in biostatistics and GWAS study. For a quality control (pre-imputation), I need to perform a chi-square test on each SNP (there are 700 000 of them) to test the deviation for Hardy-...
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29 views

Problem with classification model of genomic data

First of all, I'd like to apologize for any spelling or grammar mistakes. I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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1answer
138 views

Best practices in the selection of distance metric and clustering methods for gene expression data

I have been reading about this on various channels including here and Stack Exchange, but I'm still not sure how to choose the best approach for clustering gene expression data. As a Ph.D. molecular ...
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1answer
29 views

R: Same dataset, different units and then, chi-square test no longer works

I am a beginner in R and statistics. I conducted Chi-square test to see if there is a significant difference/relationship between two distributions. Then, I changed my units to percentage over ...
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1answer
45 views

How to plot a heat map by giving scaling the color for row-wise?

I have a selected data table for DEG and interested in plotting a heatmap by using a color gradient row-wise (without scaling or normalizing the data). Giving a color key for the whole data set is ...
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2answers
42 views

How to test if this there is a genotypic effect or time effect or both?

I have a timecourse RNASeq experiment for mutants and WT comparisons. At lfc = 2 , pval = 0.01 I have up regulated genes for genotypic comparisions ( e.g. ...
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16 views

Predicting post translational modifications(PTM) sites using SVM

I have dataset that contains 6394 samples with length of 27. Number of positive samples 3991 and negative samples 2403. I have used the sequences as features for positive-negative classes ...
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1answer
35 views

PCA on Gaussian gene expression data

I am aware that PCA done on Gaussian distributed data ensures the uncorrelatedness as well as independence of each factor. I am having difficulty understanding what the 'Gaussian distribution refers ...
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1answer
39 views

mutual information for testing set enrichment?

I've created a process that associates members of two sets, specifically codes from the International Classification of Diseases (ICD) hierarchy and the semantically richer Monarch Disease Ontology (...
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17 views

How to perform feature extraction(PseAAC)?

I am working on K-Post Translational Modification of protein. I have gone thorugh a lot of papers. But there is no detailed view of how to extract feature like PseAAC. Any python code /package is ...
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74 views

Test for significant difference of count data between distributions

I have distributions of counts of DNA segment lengths, and I want to check if a distribution has been significantly increased between "treatments" and across populations. Conceptual example: There ...
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26 views

Combining datasets when working with PCA

I'm largely a statistics novice, and I've gotten into a discussion with my lab mate about the application of PCA. Previously I've applied PCA only to a uniform dataset (results from cells all ...
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32 views

Negative binomial-distribution as background-model: How to calculate the p-value?

I would have a question to the statistics of the following paper: Bioinformatics, Volume 28, Issue 23, 1 December 2012, Pages 3013–3020, https://doi.org/10.1093/bioinformatics/bts569 Simple summary: ...
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1answer
25 views

coefficient of variation and genes highly expressed

I am a biologist, with very little knowledges of statistics. I am looking for highly variable genes from a data set. I have calculated the coefficient of variation of the expressed genes of my dataset ...
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18 views

One-hot encoded fixed-size DNA sequence as output, what loss should I use?

Suppose I have some (deep learning) model that predicts $4 \times n$ (where $n$ fixed) matrices supposedly "unnormalized" one-hot encoded DNA sequences of length $n$, and that I know the ground truth ...
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1answer
49 views

Calculating conditional probability from a query protein sequence

We know there are 20 Amino Acids('A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'). Now my query sequence is like: KAQTAHIVLEDGTKMKGYSFGHPSSVA of ...
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109 views

What is the probability of regex pattern occurrence in a string of length n?

I have a string of length n, composed of 20 characters of equal probability. What is chance of occurrence of a regular expression pattern, like 'WP[^WFHY]{5}W' by chance? In case you are not familiar ...
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1answer
46 views

Significance of differences between group-differences

Background: We have RNA-seq data (a method to quantify the expression of genes in a cell) from different cell types. These data were normalized using a method called TMM and then log2-transformed ...
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25 views

Calculating UniFrac distance

So I am trying to calculate unifrac distance for my OTU table, which has about 3000 taxa, 300 samples. Now my phylogenetic tree only consider the most important 500 taxa. My questions are: Do I ...
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289 views

Interpreting snake-like structures in the UMAP visualization of a FASTA data set

I'm looking for some guidance to interpret a UMAP plot. I started with two FASTA files for two different genes. I concatenated everything into a single string of only ACGT. Then I split that ...
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37 views

Should a statistical test be performed if power is very low?

I performed some partitioning of data set (genes) into two lists, resulting in two enrichment lists. I wanted to compare them with Fisher's test, but from before I know that similarly looking results ...
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1answer
23 views

have many error likelihoods, how to combine to get a confidence or p value?

I'm working in bioinformatics and its been a long time since I dusted on my statistics. Basically I'm working on variant calling which amounts to sequencing a large number of sequence reads and ...
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1answer
42 views

How to measure interaction between variables (mutations)?

I have a large dataset of germline genetic mutations from a population of 1,000 individuals both affected and non-affected. I've already looked into individual mutations that are enriched in the ...
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14 views

Significance test for Patient Years

Previously, I had a question about CI for Patient-Years (py) and there was a great answer from @TamasFerenci. Now I need to find out the $p$ value for the py of two different groups. I have a table ...
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1answer
70 views

Is this an example of where I shouldn't scale before doing PCA / PLS?

I'm working with NMR spectra (it's a common chemical test). There are various peaks of the signal across a range of ppm values. I'm trying to relate the NMR spectra of various samples to a ...
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25 views

Finding first statistically significant point of s curve (sigmoid function) where slope decreases?

Apologies if my title is awful. I have very little statistics experience so I'm hoping the title makes sense. Background on what I'm doing: I'm working on a program that calculates the minimum ...
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1answer
114 views

How to interpret the survival analysis results based on summary results?

I have a gene CFAP97 with expression values and clinical information like FollowupDays and patient_vitalstatus. Using the gene expression data first I classified ...
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2answers
128 views

Preprocessing gene expression dataset

Given a gene expression dataset with 99 samples and 10000 features, it is required to find clusters of samples in the dataset. Now taking the features and finding their means and subtracting those ...
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29 views

Rank non-normally distributed sets of integers: long read sequencing and phase blocks

I have about 20 arrays of empirical integer values, which are each not normally distributed, with long tails. I am looking for a 'sane and sound' metric on how to sort these distributions, "with ...
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1answer
20 views

Fusion gene detection from TCGA or ICGC data

My PhD project involves fusion gene detection from cancer data of TCGA and ICGC portals. I find that the RNAseq files (fastq,bam formats) are mainly closed access, whereas the clinical or expression ...
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1answer
35 views

Risk prediction equation for disease based on concentrations of circulating proteins

I want to derive a risk prediction equation for disease D based on Pa and Pb, where Pa and Pb are concentrations of circulating proteins in the blood. Disease D has two sub types: Da and Db. In Da, ...
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1answer
336 views

Methods for comparing two dissimilarity matrices

I have run cgMLST on E. coli isolates, then i ran the resulting allele labels through the "daisy" function in R with the "gower" setting to generate a dissimilarity matrix. I have subsets of isolates ...
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29 views

Adjacency matrix of amino-acid residue [closed]

How to get the mathematical representation of the chemical bonds in protein residue or the whole protein? Is it possible to get the connectivity matrix or a pairwise description? The example in the ...
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97 views

Why don't my GWAS QQPlots look the same?

I am trying to create a QQPlot of 100 log-transformed p values from a GWAS study. The idea is that taking the -log(p) will magnify the smallest p values to make them easier to see. (reference) I was ...
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57 views

Compare frequencies in HUGE number of categories

I have 2 samples, each with many (e.g. 100'000) different categories (colors in urn model), and counts for each category (number of balls of each color - many with few counts, and few with higher ...
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1answer
408 views

Maximal Information Coefficient (MIC) in practical bioinformatics applications

I am interested in Maximal Information Coefficient (MIC) as an alternative to Pearson correlation when looking at gene co-expression from microarray data. I've read some very good posts on this ...
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1answer
73 views

Genomics Stats 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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