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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16 views

How to get rid of background noise in time series data?

I have a load of time-depth data collected from some birds on a field trip. I am trying to classify diving behaviour by setting a depth threshold past which a dive can be said to have occurred. ...
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12 views

How do I plot multiple Pearson's correlation plots with for loop? [closed]

I have dataset from which I derived cdc15 time course experiment. My goal is dput(cdc15) ...
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1answer
38 views

Combining various annotation metrics to score genes?

A novice question. I want to score each gene based on the net score for a set of annotation variables in the columns. My aim for scoring the gene is gain an indication to the level of its impact/...
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1answer
35 views

How to summarize multiple independent false discovery rates (FDRs or q-values)?

In the context of high-throughput biological assays (e.g. genomics), where we are applying a hypothesis test (e.g. differential expression between groups of samples) to each analyte in a dataset with ...
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1answer
36 views

How to properly display technical replicates in figures?

Let's say there was an experiment with two groups that I'd like to compare, both with three biological* (n = 3) and three technical* (N = 3) replicates each. For statistical analysis, I'd average the ...
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1answer
26 views

Determining a p-value for a test statistic that depends on other test statistics

Sorry for the confusing wording of the title. If some has any better way to word it, please feel free to change it. Background For those unfamiliar with bioinformatics data, I have data from a ...
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1answer
64 views

Repeated measure with complex data structure

I have a set of age matched patients (40males and 40females). I am measuring the drug dose effect on their hormone outcome. They are treated for 4 weeks, each week we increase the drug dose starting ...
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2answers
39 views

How would I go about testing if there is any significant difference in the mean battery life between an Android phone and an iPhone?

Let's say that the following is the data for battery life in minutes for an Android phone: Android<-c(60,64,62,71,78,64,82,77,71,72,68,66,65,80,79,71,63,60,61) ...
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1answer
80 views

Cellular deconvolution intuition

Cellular deconvolution yields the proportion of cell types from bulk tissue. After estimating the proportion of each cell type, why cannot one multiply the total expression by the proportion to get ...
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19 views

How to find a virulence factor?

I have a big data set of protein expression. I just put the head of it. ...
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1answer
40 views

Analyses of Gene expression dataset, what stat test?

I was wondering if there was a way to analyse my RNA seq dataset in a way that I could work out which day the specific gene I have is most significantly expressed? I have a RNA seq dataset with 6 days ...
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1answer
68 views

Two Sample t-test with bootstrapping for gene expression matrix in R

I tried bioconductor packages for differential gene expression analysis such as EdgeR, Deseq2, Limma and obtained expressed genes by these methods. I want to compare my results with Two Sample t-test ...
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1answer
26 views

Validation on independent biological dataset

I am working in the space of cancer statistics. I am looking for reasons why it is important to validate statistical observations in an independent biological dataset. Does anyone have a list or a ...
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1answer
50 views

Cell colony survival mapping in a particular spatial pattern

I am attempting to spatially map the cell survival in a given scanned image of a cell flask. Quick background: the cells have received a high dose of irradiation (protons/X-rays) delivered through a ...
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22 views

Identity the most informative individuals in the correlation matrix

Suppose there is an n by n correlation matrix A. In this matrix, some data are related to each other (based on their genotype). For example, in the case of people, they are full-sibs or parent/progeny....
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1answer
23 views

Given a graph, test if some vertices are more connected than the background

I have a neighborhood graph of some 10k vertices (a k-NN graph of single-cell RNA-seq data). I am interested if a given set of vertices is more connected to each other than you would expect by chance. ...
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29 views

Generating Error Data

I am currently doing a project on finding the HMM parameters for a channel which takes a DNA sequence as an input and aims to output the same sequence. However, the channel has insertion, deletion, ...
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26 views

Benjamini-Hochberg FDR Correction using partially observed p-values

I am working on something called eQTL analysis. My result is extremely huge, there are about 28 million rows (with its corresponding p values) per dataset, and I have 10 dataset. I tried to do some ...
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9 views

Partitioning variance of over-dispersed count data with unequal sample size?

I am analysing gene expression data collected from 4 groups. I would like to partition the variance into within and among group components. I am interested to know how much of variance of my ...
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49 views

Is this logistf approach the right way to deal with complete separation in my logistic regression?

I am performing lots of association tests between genotypes and binary diseases. The genotypes can be very rare, and my tests often have extreme case control imbalance (e.g. 500 controls for every ...
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26 views

Is this the correct notation for the logistic regression I am trying to describe?

I'm looking for some confirmation that this is the right notation to describe my logistic regression (or advice on how to fix it). I am performing association tests between a binary disease outcome a ...
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1answer
37 views

Detrended canonical correspondence analysis in R

Is it possible to perform a Detrended Canonical Correspondence Analysis in R? Im looking to analyse ecological (pollen) data to investigate beta diversity through time. As far as I can tell I have to ...
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0answers
13 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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2answers
261 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
97 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
32 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
71 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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8 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
26 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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410 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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0answers
20 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
70 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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27 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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22 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
78 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
455 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
31 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
184 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
48 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. ...
2
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1answer
41 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
42 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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0answers
84 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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0answers
43 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
34 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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1answer
69 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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192 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
58 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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38 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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