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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10 views

Non-vector data and SVM?

My research is on antimicrobial peptide classification and prediction. I have gathered peptide sequences of lengths ranging from 10 - 200 and classified them using different machine learning ...
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1answer
23 views

What is the relationship between differential analysis and hierarchial clustering?

I'm currently in an internship for R bioinformatics, where I'm writing software for single-cell RNA sequencing analysis. We're looking for differentially expressed genes between groups, but I don't ...
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7 views

Comparing Peptide Amino Acid Composition: 2 Independent groups, Non-normal data, discrete data

I have two large groups of peptides, "positive" group (n = 368) and "negative" group (n = 880). The average length of the peptides (in each group) is about 20 amino acids. What I am trying to do is ...
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3answers
499 views

What can we learn about the human brain from artificial neural networks?

I know my question/title is not very specific, so I will try to clearify it: Artificial neural networks have relatively strict designs. Of course, generally, they are influenced by biology and try to ...
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1answer
34 views

Feature selection with genetic algorithm in R [closed]

I'm looking for a R-package that does feature selection using a genetic optimization algorithm. I couldn't find one on CRAN and I wonder whether there is a free one. I would be very appreciative for ...
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1answer
75 views

Why is SVM better for bioinformatics analysis?

I have used five different algorithms: bagging, boosting, C4.5, random forests and SVM, for binary classification of biological data relating to peptide sequence. The dataset comprised of ...
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27 views

Position Based statistics in DNA sequence

Let's say you have a DNA sequence with 21 positions, each of which can have one of four nucleotides (A,C,G,T). For example, If I see lot of C's and G's (called 'GC content') at 19th position in all ...
2
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1answer
43 views

Calculating residual DTW distance for a subset of the alignment (Dynamic Time Warping)

My question is: "How do I find the cost for each step taken using the dtw R package?" My work is below, so if you see an easier solution please point it out! DTW is very effective at aligning my ...
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2answers
30 views

Statistical test to compare paired scores

I would like to measure (to quantify with a statistical test) how much different are paired scores. For example: for gene "x" I performed an experiment with technology A that gives a score, then for ...
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1answer
29 views

Probability of a deleterious mutation, given an observed distribution of mutations

This problem has been driving me crazy for days, so I finally resort to asking for help here: Consider a set of genes, where each gene consists of a sequence of letters, for example ...
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0answers
19 views

Finding outliers across experiments

I have data across six different biological experiments (of varying pH levels) for around 150 different cases (but not all cases are found in each experiment), looking like this: ...
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46 views

How do I do RLM normalization in R?

I have a combined dataset of 123 samples and 9,482 features (expression levels of antibodies from Invitrogen's ProtoArray v5.0). Based on ...
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1answer
31 views

Meaning of confidence interval refered to standard deviation

I was reading a proteomic paper few days ago and I got confused on one aspect. In the paper is written: "The global mean and S.D. of protein ratios (47-1/D3) were calculated for each replicate. The ...
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51 views

BayesA, BayesB, etc

I would like to get a plain English explanation of BayesA, BayesB. I found that a lot in bioinformatic literature but found nothing in Wikipedia, etc.
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39 views

nested multilevel model for differential expression analysis

I have read several other postings regarding nested models, but they did not seem to exactly capture my particular case, and I'm a bit unsure how to proceed with analysis of my model. Any help would ...
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0answers
24 views

Can Anyone explain the significance of Q-mean value?

I have been using the Swiss Model for modelling protein structures. It returns the modelling result with the estimation of nativeness of the structure through the Q-mean4 value. I have even read the ...
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0answers
23 views

Separation of Two Sub-populations

Background: I have a large table with 7683 rows and 42 columns containing features of cells (endothelial cells), relating to their morphometric characteristics, for example the cell area, the longest ...
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0answers
14 views

DNA sequence classification

I have a database of 3190 instances of DNA consisting of 60 sequential DNA nucleotide positions classified according to 3 types: EI, IE, Other. I want to formulate a supervised classifier. At the ...
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1answer
55 views

Benjamini-Hochberg and GEO2R

I'm currently using GEO2R to analyze a microarray data set. There is an option to generate the 250 most statistically significant genes, which calculates an adjusted p-value using the ...
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0answers
15 views

Modeling Switch-Like vs Continuous Signal

I'm currently trying to figure out the best way to model a given scenario, but am unsure of the best way to go about it, so I'll explain the situation in as much detail as possible. So I work in a ...
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22 views

conditional analysis and gene-wide analysis

I have a project where there is a list of genome-wide significant SNPs and we are interested in performing fine-mapping using only the summary stats data of GWAS. I was suggested to do a conditional ...
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0answers
15 views

selecting genes specific/agnostic to condition

I have a microarray transcriptomics experiment. The design of which is something like this : ...
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0answers
57 views

Distribution of large set of fold changes

My background in stats is limited to a few undergraduate classes. However, I have a question that intuitionally seems to have a statistical answer. Let me describe my intuition first. I do systems ...
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0answers
72 views

binomial test for over-represented kmers in biological sequences - what is the right test?

Imagine you have a long string, like a genome, and you split it up into every overlapping word of size n. This is called a kmer. ...
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15 views

Heterozygosity and the Wright-Fisher model

I was reading the textbook [Probability Models for DNA Sequence Evolution][1] by Durrett. In chapter 1, he discusses the Wright ...
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2answers
98 views

How can I evaluate my model when the the testing data are too few and the generated results don't match testing data

I have a bioinformatic data set includes a very large negative examples (let's say 30000 examples) and just a few positive examples (let's say 150 positive examples). Since I need to feed an enough ...
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0answers
16 views

Is there any bioinformatic databases gallery webpage like that of biocViews of bioconductor? [closed]

I think typical bioinformatician will keep a bunch of database files on their computers, so what are they? And how do they normally use (access) them?
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0answers
62 views

Correcting for multiple testing on non-independent sliding windows

Question Values taken from adjecent windows in a sliding windows are corrolated. If I calculate a p-value from each window, how can I correct for the fact I have tested many windows, given that the ...
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29 views

Un-smoothing/scaling (help normalizing data)

The context of this is matching experimental RNA SHAPE data to theoretical models of base pairing probabilities. RNA folds back on itself, some bases pair with each other, and some bases remain ...
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26 views

Repeated multiple regression for LASSO significance testing

I'm currently working on a statistical modelling problem in biology. We have cellular measurements of proteins in every cell in a tissue, and I'm using regression analysis to see if a given protein is ...
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1answer
132 views

How to calculate degrees of freedom for chi squared test

I am very new to stats, and if the chi squared test is not the best way to handle this, please let me know. To simplify what I'm trying to do, I have many separate lists of genes. Each list is a ...
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1answer
124 views

How do I calculate the p-value in a gene enrichment analysis, using parametric and non-parametric methods?

I have a list of 20 QTL from an experiment involving a certain phenotype related to bone development. Of all the candidate genes within the 20 QTL intervals, 5 are associated with a certain disease ...
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1answer
52 views

Needing help in order to infer the statistical hypothesis tests performed in an old paper

I am in great need of help in order to infer the statistical hypothesis tests performed in an old paper. However I need to make some reasonable guesses only from the abstract of the paper since the ...
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0answers
151 views

“Robust” normalization of features from multiple groups and unknown distributions prior to learning

I'm working on a machine learning project involving statistical analysis (and later discriminatory classification) of different proteins (samples) drawn from multiple, potentially overlapping classes ...
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1answer
72 views

A Conditional Probability Problem

This is a biological problem, however the problem requires a statistical solution, so therefore I'll keep it as abstract as possible in order for statisticians to be also able to contemplate it - I'm ...
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1answer
22 views

What is a nonreductive database?

A database like Genbank is said to be a nonreductive database. What does that mean ?
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1answer
162 views

Why genes are assumed to follow multivariate normal?

I wonder why gene expression data are very frequently modeled by multivariate normal distributions. What is the reason for those strong assumptions that the genes follow multivariate gaussian? Are ...
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0answers
36 views

Biostatistics - sampling size [closed]

I am interested in discovering motifs in a set of DNA sequence(say 100) and I would like to use the approach of using a subgroup(say 10 from 100) and likewise create random subgroups(picking 10 from ...
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48 views

review papers on P-values, adjusted P-values and common statistical tests in bioinformatics

I'm looking for review papers which give comprehensive reviews of P-values, adjusted P-values and common statistical tests in bioinformatics.
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73 views

How to justify using a gamma distribution for biological image analysis

I am trying to characterize objects within the nucleus of a cell. These objects are brighter than the background, and when I remove the background and map the frequency distribution of the objects I ...
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2answers
113 views

GA or ANN, and suggestions

I am working to approximate, to extrapolate rather, values of a function from a few known values. Here is what I have: Less than 100 known I/O pairs. A monotonously positive correlation.en Something ...
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1answer
117 views

How can to compare 1750 samples between 3 groups by R?

I have 1750 proteins that I want to compare the expression level of them between 3 groups (cell-type) using R. How can I do it?
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2answers
77 views

Phylogenetic tree with known historical sequences?

I have a multiple sequence alignment that I'm using to construct a phylogenetic tree. Usually, phylogenetic trees are constructed under the assumption that the input sequences are all from the present ...
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1answer
36 views

Given a matrix, each row with a list of numbers, find the most variable rows with an “interesting” pattern

I have a file that can be considered as a matrix with each row representing a measurement of gene expression of different samples (each column is a sample). I want to find those genes with the most ...
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1answer
380 views

Bootstrapping of RNA-Seq data: normal distribution?

I have an RNA_Seq dataset (FPKM values) obtained from the ENCODE Caltech datasets for K562 cells; I also have 6 different lists of genes and I want to show that the expression values of my panel of ...
5
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1answer
327 views

How to compare two groups when one only has one data point? [duplicate]

I have two groups I want to compare, however, I only have one data point in the first group compared to 450 data points in the second group. Here's the story. I have a patient that has a mutation in ...
3
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2answers
319 views

Assumptions in estimating probabilities from a contingency table

Say I have a database with 10000 protein sequences of the same species in it. I was to study if mutations at positions i and ...
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4answers
3k views

How to do 4-parametric regression for ELISA data in R

I am a biology student. We do many Enzyme Linked Immunosorbent Assay (ELISA) experiments and Bradford detection. A 4-parametric logistic regression (reference) is often used for regression these data ...
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58 views

General rules for forming groups for analyses

I am analysing EEG data. I have data from 19 electrodes from 25 participants divided into two groups (11 and 14 subjects). I asked my student to compare these two groups with some statistical test. ...
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1answer
141 views

Limit of quantile normalization

Is quantile normalization adequate for normalizing data with very few samples? For example this microarray data. Typically after normalization we'd like to compare ...