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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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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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Overdispersed proportion test?

I am comparing proportions in genomic data. In particular, I compare two populations, A and B, and I look at genetic sites. In other words, I have N contingency tables ...
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Normalization of LC-MS data

I am working on a metabolomics project. I am very new to the world of metabolomics. I have been provided an LC-MS dataset in which all the injections are done with the same concentration of the ...
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13 views

The difference between the cumulative baseline hazard and the cumulative hazard?

I'm not sure what is the difference between the cumulative baseline hazard and the cumulative hazard? Could you please explain it if you are an expert in this field? Thanks
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1answer
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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
39 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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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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20 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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39 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
63 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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19 views

Shotgun sequence statistics

I trying to understand the statistics behind shotgun sequencing. Below is an excerpt from a book. Can anyone tell what does the below bold sentence mean? I did not understand the interval range and ...
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1answer
32 views

A question about pca and gene function analysis

I'm new to bioinformatics, and I have a pretty basic question. Let's say I have a bunch of genes {Xi} and I want to know which one has the most significant on some measurable phenotypic trait Y. Now I ...
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Enrichment analysis--what does this psi mean?

Here is a figure taken from this bioinformatics paper. It's describing the "Deviation of the cumulative distribution from uniform of the scaled ranks", but it doesn't explicitly tell me about what $D(...
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test on fold change of the mean vs. mean of fold changes [duplicate]

Suppose we have 5 subjects. For each subject, biomarker is measured at t0, t1 and t2. Measured values are skewed. We want to compare the values at t1 and t2. When we have skewed data, usually we do ...
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9 views

How to find which type of SV occurs most in a gene?

I am interested in a gene. I have data of what types of structural variants occur in this gene for a patient population (n=300). This gene in total has 200 deletions, 150 duplications, 10 inversions ...
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About standard deviation expansion

Recently, I read an academic paper. There was a formula that I could't understand. SD represents standard deviation, n (n+1) represents the number of samples. Does anyone know how this formula is ...
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1answer
50 views

What does it mean to apply k-means algorithm on transformed distance matrix?

I am reading a very good (recent) publication in clustering: Kiselev et al., 2017, SC3 - consensus clustering of single-cell RNA-Seq data (if you don't have access, see author PDF). The algorithm ...
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1answer
18 views

Background selection in hypergeometric test using diferent cell types

I have to select the background for an hypergeometric test that I have to perform. The problem is as follow: I have a list of genes differentially expressed in cell B between "control vs treatment"....
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Difference in library size in next-generation sequencing and differential expression analysis

A common observation in the next-generation sequencing experiments (eg. RNA-Seq) is the difference in the total number of uniquely aligned reads between experimental conditions that we want to compare....
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2answers
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What kind of Statistic Method for enrichment or overrepresent should I used for a rank ordered vector with Binary status

I have a gene expression data from 1065 different cell lines, let's say "BRAF" gene. BRAF gene expression levels are ordered. Most TP53 mutated cell lines are high BRAF expression (see the figure ...
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1answer
20 views

Pearson's Correlation on high throughput micrroarray data

I am working in bioinformatics. I am using a microarray data of 24000 genes (attribute) and 170 samples. Is it possible to find Pearson's correlation of 24000 attributes?
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31 views

Probability of observing certain data given prior knowledge

Background: I am building a framework to analyze a type of experiment called protein microarray. The basic idea is that you can affix a bunch of different proteins on a microarray chip and then apply ...
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1answer
12 views

Antisense Transcript Level

The basic biology says genes on the DNA, get transcribed to mRNA (sense transcription), and the RNA will be translated to proteins. but sometimes, a gene can have transcription from the opposite ...
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Modelling different types of responses to a series of drug concentrations

I have been performing dose response experiments on cancer and control patients for cell counts, apoptosis (flow cytometry DAPI-AnnexinV staining), intracellular protein staining on flow cytometry and ...
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Regression relating means and variances in DESeq2

In the DESEq2 algorithm for analyzing RNA-seq data for differential expression, a key hypothesis is that the means and variances of the count data, assumed negative binomial, for the individual genes ...
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1answer
29 views

How to calculate correlation of 2 variables combined

I have data on 2 histone marks that influence chromatin density. I have calculated individual correlation scores using the cor.test() function in R for both. I would like to combine the 2 together to ...
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1answer
28 views

biological fluorescence supervised machine learning [closed]

Some general questions... So it appears with most classification learners one must come up with a series of quantifiable variables to associate with each observation. This might include mean and std ...
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23 views

Statistical test for determining hot spot in a heat map

I'm analyzing high through proteomic data and have several thousand 5x5 matrices, where in each matrix the rows and columns refer to different biological conditions, and each cell refers to gene ...
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1answer
211 views

HMM depmixS4 using a vector of known states to fit model

I am using the depmixS4 package to fit HMMs to RNAseq count data. My workflow is as follows: Stack reads into a 'stack' vector which looks like this: ...
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34 views

Batch effects in survival data

I have a problem concerning batch effects in survival data of C.elegans. I read through a few forum posts and a paper but I am still not really getting it. In the experiment the effect of different ...
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0answers
9 views

Substitution model for maximum likelihood in linguistic phylogenetics?

When using maximum likelihood to estimate a phylogenetic tree on the basis of linguistic data, is there a standard substitution model that one should use?
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0answers
25 views

How to download SNP data from specific regions, population and positions?

I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems. To do that, I've read a lot of papers and books in order to understand the main ...
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27 views

Selection of differentially expressed genes

I don't have any statistical background. Have some questions. I see in some research papers they select differentially expressed genes based on fold change and p.value. And in some other papers I ...
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312 views

How to code a model with the adonis function in R (permanova) for a paired/matched design (epidemiology study)

We have a database of 100 children that are grouped in 50 paired/matched groups (of 2 children) based on co-variables such as sex, c-section, and antibiotic treatments. We obtained the gut microbial ...
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247 views

Kamada Kawai vs Fruchterman Reingold

I am trying to visualize microbial correlation networks. I am using igraph in R. And my goal is to have weighed edges based on the correlation coefficient between the nodes. I don't understand what ...
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1answer
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Can a Random Forest model trained on an NxM feature matrix be used to predict outcomes on a new feature matrix with k overlapping features?

Context: I'm familiar with the basics of Random Forests, and I'm currently implementing a random forest classifier to make predictions on new proteins using sklearn's ...
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76 views

How can I only use some of the interaction terms for an ANOVA in R?

Data Background: The data set contains growth data for 4 species of plants in two different soil types. I want to see if the soil type has an effect on plant growth, but I know a priori that the ...
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1answer
403 views

Artificial neurons based on modelling observed correlations and predicting from them?

Biological neurons are much more sophisticated than standard ANNs. Basing mostly on received impulses, they can learn long correlation chains between e.g. visual cortex, motor system and motivation ...
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1answer
105 views

Controlling FDR when p-values are bimodal

I have a quick question about using the Benjamini-Hochberg procedure to control FDR using the p.adjust() function in R. I have read that in order to properly apply ...
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1answer
296 views

How can I analyze multi-dimensional (concentration, time, …) dose-response data?

I have data where different compounds were applied to cells and a numerical readout was measured. Each compound was used at multiple concentrations The readout was measured at multiple points in time....
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1answer
152 views

Compare distances between real data and simulated data

I have some data that shows the distance from a position in a genome pos to the nearest location (min_dist) of a genomic feature ...
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123 views

R: missing interaction in summary table, binomial GLM + type iii errors

I am confused as to why my summary table is missing NeonicfCLO and Treatment:NeonicfCLO? I guess it has something to do with ...
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1answer
314 views

Boxplot GLM with binomial errors - interpret summary

My apologies, I am not even sure how to phrase this question clearly. I am essential trying to get meaningful statistics to present tomorrow. All I have managed is this. However, I am very confused ...
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1answer
248 views

How to Implement Biological Neuron Activation in Artificial Neural Networks

In artificial neural networks, activation functions are used for neurons, i.e. the sigmoid activation: Which can be implemented in code as (in Python): ...
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Does ordering the comparisons by p-value make sense?

In bioinformatics I usually do enrichment test (read hypergeometric test) with many comparisons over the same list. After correcting for multiple comparisons I usually order the results by p-value (...
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2answers
39 views

Which statistical test to choose - protein analysis

First I will describe my problem (1), then solutions I found (2), and then pose the question (3). 1) I am a student making a simple program for statistical analysis of data for a biological ...
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2answers
873 views

Why does log-transformation of the RNA-seq data reduce the amount of explained variance in PCA?

I am running a PCA on a dataset with 2k rows and 36k columns. I noticed that when I log-transform the data I need to ask for more principal components during PCA to achieve the same amount of ...
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1answer
56 views

Single-cell RNA-seq: deep & few or shallow & many?

My lab does a lot of single-cell RNA-seq. Our goals are to find out what cell types are present, characterize their gene activity, and (if possible) understand how the different subpopulations are ...
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1answer
40 views

Is there a way to identify the characters/variables that have the greatest impact on the inference of a phylogenetic tree?

I have a dataset of molecular sequences from which I have inferred a phylogenetic tree (a.k.a a dendrogram) with various algorithms (maximum parsimony, neighbor-joining, and maximum likelihood). What ...
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2answers
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Continuous generalization of the negative binomial distribution

Negative binomial (NB) distribution is defined on non-negative integers and has probability mass function$$f(k;r,p)={\binom {k+r-1}{k}}p^{k}(1-p)^{r}.$$ Does it make sense to consider a continuous ...