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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38 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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8 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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67 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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35 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
19 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
42 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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0answers
21 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
26 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
58 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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0answers
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
14 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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21 views

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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20 views

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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49 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
30 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
91 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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0answers
22 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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0answers
40 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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45 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
158 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
72 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
37 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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16 views

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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27 views

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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0answers
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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20 views

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
60 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
23 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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26 views

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
31 views

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
23 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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1answer
13 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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18 views

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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1answer
49 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
29 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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1answer
47 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
288 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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0answers
39 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
35 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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0answers
435 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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0answers
314 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
48 views

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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1answer
406 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
142 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
366 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
213 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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0answers
165 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 ...