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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Why use sliding window input features in sequence modeling?
I was reading through the DNABERT paper and found that their input features were k-mers. This is equivalent to using rolling/sliding window features in the other common family of sequential problem, ...
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Bias in the normalisation of gene expression due to low counts
I hope it is okay to ask a question because I am one of the silent user or this forum. My background is in biology and I am not so confident in my skills in stats
The goal of the analysis is to ...
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Linear modeling of pseudobulk: how to model multiple types, conditions, and timepoints
I have pseudobulk gene expression counts from multiple celltypes that I want to perform differential expression testing on. The study includes a treatment, a pre and post treatment timepoint, and ...
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Running all possible fixed effects combinations, LMER, PCA [duplicate]
my data looks like that:
...
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Running all possible fixed effects combinations for linear mixed effects models
my data looks like this:
...
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Logistic Regression to identify significant covariates(variables)
I am working on logistic regression to identify the most cucial genes that can predict the response of stimuli.
I have a workflow that looks fine to me but I want inputs from the people who have more ...
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Optimization of SOM grid and number of metaclusters flowSOM
I am currently attempting to optimize the dimension of the SOM grid, as well as the number of metaclusters for some flow cytometry data in R, using the well documented flowSOM package.
From what I ...
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Methods to identify a latent sistematic source of noise
I am working on modeling the relationship between various biomedical variables (age, sex, diseases ...) and DNA methylation data. DNA methylation data consists of percentages of methylation at many ...
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HMM matching a string as mosaic of two strings from a larger panel
I have a problem which I think can be solved by an appropriately structured (“constrained?) HMM, but I’m not sure how to structure it, and what the prior art is. Any help such as implementations, ...
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Is there some way to analyze nominal data with repeated measures when there is a very small sample size?
So I have some data of 16 patients who were subjected to a test a different number of times (some only once, some as many as 7 times). The response variable is definitely nominal (I wasn't involved in ...
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Making use of relative density of genomic features between gene sets
I am looking at a particular genomic feature in two sets of genes: set A is a positive control set, where I know this feature is overall enriched in the genomic DNA of these genes, and set B is a (...
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The relationship between prediction performance and the degree of association between variables?
I've been reading a paper (Machine learning identifies candidates for drug repurposing in Alzheimer’s disease), but having a hard time understanding its core idea. Basically, the researchers
Obtained ...
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Statistical significance in known population
I am working with a data set with the sequence identity (a value in [0,1] representing the conservation between sequences) of many genes for many bacterial strains. I would like to be able to draw ...
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How do I use a chi squared test for homogeneity/other statistical method for this situation?
I am performing analysis on data of ~8,000 patients who have COVID. This is my scenario. I have information of each patient being classified as either severe or non-severe in how COVID-19 affected ...
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Estimated standard deviation of a phenotype prevalence that is derived from several studies
I have allele frequencies from two independent studies
Study
Number Sample
Allele 1 Freq
Allele 2 Freq
Allele 3 Freq
A
20
.45
.475
.075
B
34
.72
.28
NA
The weighted average of each allele ...
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How to test differences (over time and between treatments) of a specific species in DNA metabarcoding sequencing data?
I have DNA metabarcoding sequencing data in the following format:
plot
Time_point
reads_species_A
Reads_species_B
reads_species_C
1
T1
0
245
65
2
T1
48
455
0
3
T1
15
5
10
1
T3
153
23
564
2
T3
...
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Weird Cooks distance results using DESeq2
I'm currently trying to assess fold change when comparing two different sample types using DESeq2 package and I'm getting weird Cook's distance values which are causing major problems.
The two ...
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Comparing microRNA expression at different tumour stages and identifying trends in miRNA expression
I'm currently working on a university project using publicly available data. I'm collecting genome data on cancer patients at different pathological stages (Stage I, II, III and IV).
I'm aiming to ...
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Reference request for books on statistical methods in Bioinformatics with exercises and solutions
I have acquired the book Statistical Methods in Bioinformatics: An Introduction by Warren & Grant (2004 edition).
There are exercises in the book, and I would like to try and solve them but there ...
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Handling ties in Cox regression using Peto-Breslow method, is the derivative of the log likelihood correct here?
I am trying to implement Cox proportional hazard model in Python. Although, I know how to calculate the derivates of the Log likelihood, in the case of ties the likelihood function is modified. So I ...
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Correlating a continuous clinical variable with multiple measurements per sample with a gene signature?
I am trying to correlate a continuous clinical variable with gene signatures from single cell gene expression data. I used the UCell package in R to create a score (on the y-axis) for each cell from ...
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What is the appropriate statistical test to assess position within a distribution?
I am doing a bioinformatics analysis, where I am scoring every protein-coding gene in the human genome (~19,000) for some genomic property ("interestingness"), then plotting the distribution ...
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How do I combine/format experimental replicates when checking for normality
My data is currently structured like this:
| ID |bio_rep1|bio_rep1 |bio_rep2|bio_rep2
|path1| 1002.4 | 1032.2 | 340.2 | 528.5
|path2| 1004.6 | 1045.5 | 0 |88
My data is ...
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What are the effects of adding technical/pseudo replicates to the ones to be deconvolved?
I want to perform deconvolution of a small data set (3 samples of one conditions vs. 4 of another). The tool CibersortX can estimate the sample-specific expression of cells, using the bulk expression ...
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How to normalise sequencing and qRT-PCR data for joint correlation analysis
We would like to analyse the correlation between cytokine (IL-6) and miRNA expression.
However, we quantified the cytokine level in samples, in which the miRNA expression was quantified using either ...
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53
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Problems understanding design matrices and matrix models
I have to analyze gene expression data acquired by DNA microarray experiments. Unfortunately, I never had a good lecture on statistics, which is why I'm often struggling with data analysis.
The ...
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Do we assume independence among individual observations in a hypergeometric test?
Commonly, the hypergeometric test and Fisher's exact test are two main statistical approaches used when computing a gene set enrichment for a functional term (e.g., among the top 10 differentially ...
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49
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Wilcoxon test for unrelated samples
I have a cancer dataset with two groups of patients, those who responded to the therapy and those who did not.
I run cell type enrichment analysis, to get an idea of the cellular structure for each ...
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Derivation of factors associated with increase in HIV DNA
I would just like to verify a statement made in the following paper: Peripheral blood HIV-1 DNA dynamics in antiretroviral-treated HIV/HCV co-infected patients receiving directly-acting antivirals
The ...
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First principal component separate the clusters but other PCs not
I have two sets of vcf files with different samples but from the same population. I merged the two and want to compare the two sets via PCA analysis.
Since the two set is from the same population I ...
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Statistics for large k-mers with low counts
Suppose I have a big genome and a small one (ex. mitochondrion) And I would like to know which words or k-mers of length k (ex. "AGCCGTA" - k = 7) are under/over-represented in both genomes, ...
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How to statistically test correlation and coincidence between two negative binomially distributed sets of counts?
I am working with novel Next Generation Sequencing (NGS) method which reports DNA breaks with perfect single nucleotide-resolution and strand-specificity. The outcome of the technique is that the ...
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2
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Dealing with NAs in genomic data statistics
I have done a GC content (counting C and G in genomes) and GC variation within genomes, in a slide-window (1000 pb-base pairs). I have each genomic data separated in tsv files. When I work with pandas ...
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confidence intervals of a biological assay
Given my work on ICeChIP (a biological assay that measures the binding of one, two, or more proteins along the genome)
https://github.com/shah-rohan/icechip/blob/master/Scripts/computeHMDandError
I ...
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Should I correct for batch effect before selecting features using random forest for RNA-Seq data?
This is a mix of bioinformatics and ML problem. Hope someone with both expertise can help. Please forgive me if it's unclear or I used the wrong words as I am very new to ML.
I am trying to pick out ...
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49
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Alternatives to ANOVA for kill assay
I'm trying to find an appropriate test to compare my data. I ran a 2-way repeated measures ANOVA to compare different drug concentrations' effects on bacterial population count at different time ...
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Alternatives to ANOVA for kill assay [duplicate]
I'm trying to find an appropriate test to compare my data.
I ran an ANOVA to compare different drug concentrations' effects on bacterial population count at different time points. I believe that the ...
Jamie rowland
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1
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113
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Loess regression on genomic data
I am struggling with R loess function in R.
I have a dataframe on which I would locally weighted polynomial regression
For each ‘Gene’ is associated a Count (log10 transformed) which gives information ...
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297
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Design and contrast matrices for analyzing the effect of two factors of interest on protein expression, controlling for factors and covariates
I've posted this question on the Bioconductor support site but haven't received any responses so I figured I'd try here. The post was quite detailed so I'm copying it over mainly as-written. Please ...
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Killing assay analysis [closed]
I have a bacterial killing assay with 3 drug concentrations and one control. I have data for 6 time points including time point 0. I want to use statistical tests to compare the control to each ...
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1
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When predicting case status, what is the appropriate way to examine differences in proteomics by gender (/the interaction between protein and gender)? [closed]
I have a dataset I'm working with containing measurements of several thousand proteins per person, with about 150 people split pretty evenly between two groups (cases and controls). Case status is ...
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Correct batch effects using R limma package
This is a bioinformatics question I hope there are bioinformaticians in the crowd.
I know that batch effects are variations in the data that are not biological, but from outside factors, like who took ...
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A case to avoid a linear mixed effect model
This is a simplified explanation of my experiment, for those not familiar with single cell RNA seq.
24 small chunks of brain were taken from 12 diseased people and 12 normal people. Gene expression ...
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parallel lines (cluster) in PCA plots (PC1 vs PC2)
There are about 20 subjects, 3 treatment groups, and 1000+ genes in my data; the 1000+ genes were processed in two batches. Could anyone comment on why I am seeing parallel lines/clusters in the PCA ...
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301
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Number of variables to include in my GLM and how to interpret the surrogate value analysis
I am working with genes and I am designing a model that its dependent variable must be diagnosis, whereas the rest of potential variables to include are sex, ethnicity(2 levels), rin(RNA integrity ...
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Should I use a two-tailed t-test to generate p-values?
I have a data set similar to the one below. The real data set has 89 values in each column. I'm looking at the expression of RNA between two different treatments (treatment $X$ and treatment $Y$).
<...
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Estimating Best Solution to Linear Equation
I believe this is quite a basic question, but want to make sure I'm doing this properly.
I want to solve the following set of linear equations:
$\text{RNA}_{1}=\text{RNA}_{Tumor}*\beta_{1}+\text{RNA}_{...
2
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1
answer
959
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How to provide the fold change value of a group of biological replicates?
I want to visualize relative gene expression with barplot + error bars after qPCR analysis. I was asked to use the log2FoldChange values for the barplots, where each bar should summarize 3 values (the ...
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I have to adjust p-value in One way ANOVA with 3 groups and 600 metabolites?
I have three groups: CC, CT and TT and 600 metabolites.
When I do a lot of t-tests, I have to adjust the p-value, for example with fdr, but when I do a ANOVA with 3 groups, have I to adjust the ANOVA ...
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1
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A question for data scientists about Deep Learning Thesis [closed]
I am writing because I would like to ask more experienced people in Deep Learning about the (possible) topic of my master's thesis. I am not sure if it is not too complex and even possible to finish ...
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