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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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Perfusion Analysis Counts as Survival Analysis?

In perfusion analysis, the patient is injected with some dose of medicine. A machine detects, over time, the dose of medicine in the patient's body. In other words, the data for each patient is time ...
温泽海's user avatar
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calculating percentage normalisation

Please don't laugh or close this post I am confused as to how I can calculate the percentage normalization occurring post treatment. So, here is a background of the problem, I have reading from ...
Angelo's user avatar
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Linear models to compare SNP categories between patients

I have 8 patients (GROUP: 3 healthy, 5 disease). For each patient, I determined single nucleotide polymorphisms (SNPs) and annotated the effect of the SNPs (EFFECT_CATEGORY). Each SNP (~3000 per ...
BackFish's user avatar
1 vote
1 answer
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How to perform a power analysis for poisson distributed data

I want to perform a simplified power analysis to determine how many cells (samples) to have in control and experimental conditions (assume equal n across conditions). For an alpha level of 0.05, 0.95 ...
Cadmus's user avatar
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Input on methodology for analysing publicly available medical datasets

I'm being asked to analyse a publicly available medical dataset of adverse drug reactions. My data quality is quite sparse to begin with, so I've been trying my best to extract something meaningful ...
Mman231000's user avatar
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How to interpret AggregateExpression() in R?

I am new to scRNA-seq analysis and cell type deconvolution. I am attempting to create a 'pseudobulk' matrix (where rows = genes, columns = cell types, and cell values = TPM) from my scRNA Seurat ...
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100 views

Multidirectional propagation of biological neurons - could/should we recreate it e.g. with joint distribution neurons? [closed]

While ANNs are rather trained for unidirectional propagation, action potential propagation in biological neurons is symmetric e.g. ”it is not uncommon for axonal propagation of action potentials to ...
Jarek Duda's user avatar
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SNNs with low-moderate data requirements?

I've been looking into utilizing a survival neural network for my dataset, but am having difficulty finding a model that works with my relatively low amount of data. I have ~10 datapoints for ~300 ...
Epic Cabbage's user avatar
1 vote
1 answer
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Pseudoinversion giving poor predictions, converges with smaller matrix

I'm having an issue where running pseudoinversion as a means of predicting the values of certain phenotypes using methylation data gives extremely large numbers, very pooly predicting said values, ...
Epic Cabbage's user avatar
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Help deciding the number of components for PLSDA using mixomics

I have a lipidomics dataset with more than 1800 features and 30 samples and I want to apply PLSDA. So, I used MixOmics to do this and here is my code: ...
Proffagelle's user avatar
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Interpret UMAP distances with a single cluster

I have a question regarding the distances between points (RNASeq samples) within a single UMAP cluster. As far as I have understood, the distances between clusters can not be measured in a specific ...
user408524's user avatar
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Weighted summing time associated data for univariate model?

I have a situation where I have several mice A, B, C, etc., each of which has several thousand datapoints, all associated with a timepoint of 1 year, in addition to a single datapoint associated with ...
Epic Cabbage's user avatar
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Best practices for correlating clinical variables with gene expression data

I am working on gene expression data from humans and disease models, where I want to correlate important measures of disease severity, i.e. clinical measurements, with the gene expression. I am trying ...
A Marstrand's user avatar
2 votes
2 answers
65 views

p>>>n problem how to navigate?

I have a DNA methlation data for 32 samples. For each sample I have DNA methylation avaialble for >10000's of cpg bases (ie C nucleotides on DNA). I also have gene expression data from which I have ...
Saad Khan's user avatar
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Statistical Genetics - How to interpret data & analysis

My question is how to interpret $G_{ij}$ in the following statistical genetic model $$h(\mu_i) = \alpha_0 + \alpha'X_i + \beta'G_i,$$ where $G_i = (G_{i1},\dots ,G_{im})$ are allele counts (zero, one, ...
Kevin's user avatar
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1 answer
139 views

Adjusting for multiple comparisons after Kruskal-Wallis

I am comparing biomarker levels (50 total) obtained from immunoassay in a cohort divided into 3 groups (control vs. inactive vs. active). I want to use the Kruskal-Wallis test with Dunn’s test to ...
NG0429's user avatar
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4 votes
2 answers
117 views

How to check linearity of a variable without plots/graphs in R?

I'm running a longitudinal study comparing patients with a lung growth which either developed into cancer (cancer_status = 1) or didn't (= 0). Here is some example randomly-generated data in the same ...
bmr's user avatar
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How to analyze data which has varying amounts of measurements recorded?

I'm doing research which involves data pertaining to the physical characteristics, recorded at consistent intervals, of mice, with the mice's time at death being recorded as well. As such, some mice ...
Epic Cabbage's user avatar
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Which dissimilarity index to use with categorical ecological data [duplicate]

I am currently working on data representing the abundance of microorganisms in a categorical way, like 0 = no organisms; 1 = 1-5 organisms; 2 = 6-10 and so on (5 being the highest number). And i am ...
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Hoe to choose a spline for expression data (mRNA and proteins)

I'm using timeOmics to model a time series of expression data on mRNA and proteins data. The amount of samples is rather small (7 groups, 2-7 samples per group) but the features space is rather large (...
Sebastian Hesse's user avatar
1 vote
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39 views

Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change calculated

I have a microarray dataset that has already been normalized, and the fold change values for each gene in the mutant versus the wild type have been calculated. I'm interested in determining the ...
ucb's user avatar
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Analysis for many Categorical and one Continuous trait

My dataset contains multiple nominal non-binary variables (i.e- beak shape type, general eye position) which are represented/coded as numbers. For instance, for 'beak shape type' there are 4 options, ...
Batro's user avatar
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Distinguish causal effect from vitamin supplementation from natural vitamin on negative outcome from vitamin supplementation

Hi I will be very grateful for any help or ideas or hints. I have searched the internet but no suggestion seems to be able to help me. I am a bioinformatician and I mostly work with R. I have a ...
Charles's user avatar
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Why my GWAS p-value QQ-plot falls far above diagonal? [duplicate]

I'm trying to run GWAS pipeline using plink, but the results I got look really off. The QQ-plot of the p-values is far above the diagonal. I'm pretty sure I followed the correct QC process, and the ...
Celia L.'s user avatar
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1 answer
101 views

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, ...
Avatrin's user avatar
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1 answer
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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 ...
black_cleaver's user avatar
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17 views

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 ...
Derrik Gratz's user avatar
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0 answers
22 views

Running all possible fixed effects combinations, LMER, PCA [duplicate]

my data looks like that: ...
Chemokine1's user avatar
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26 views

Running all possible fixed effects combinations for linear mixed effects models

my data looks like this: ...
Chemokine1's user avatar
1 vote
1 answer
57 views

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 ...
Angelo's user avatar
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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 ...
h3ab74's user avatar
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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 ...
SunScript's user avatar
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146 views

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 ...
maglorismyspiritanimal's user avatar
1 vote
0 answers
15 views

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 (...
C. Murtaugh's user avatar
3 votes
1 answer
42 views

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 ...
h088bmIuXaskpzJEe3ld's user avatar
1 vote
1 answer
43 views

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 ...
Rachel's user avatar
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2 votes
1 answer
64 views

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 ...
Mather123's user avatar
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1 answer
44 views

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 ...
curious's user avatar
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1 vote
1 answer
66 views

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 ...
Robvh's user avatar
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1 vote
2 answers
371 views

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 ...
Miguel's user avatar
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1 vote
1 answer
23 views

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 ...
user378714's user avatar
1 vote
1 answer
397 views

Ranking genes within GSEA

I know you can rank genes by p-/q-value, or by log2 fold change. But can you combine the two methods somehow? I have read about combining fold change and p-value here but what is one advantage and one ...
katara 's user avatar
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0 votes
1 answer
741 views

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 ...
Saashe's user avatar
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0 votes
1 answer
49 views

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 ...
Muchomaas's user avatar
0 votes
1 answer
91 views

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 ...
C. Murtaugh's user avatar
2 votes
2 answers
162 views

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 ...
Sam's user avatar
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0 votes
1 answer
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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 ...
Osgarion's user avatar
0 votes
1 answer
75 views

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 ...
Sam's user avatar
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0 answers
59 views

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 ...
Programming Noob's user avatar
1 vote
1 answer
28 views

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 ...
h3ab74's user avatar
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