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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7 views

A rate model for sodium channels

I am studying by myself Human Physiology. I have encountered the following question: In the following given model of sodium channel with 3 states open closed blocked (which I assume means ...
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14 views

Mutations in known DNA sequence: which test to use?

I am analysing a double knockout (mouse), and trying to see whether restoring one or another of the genes it's missing affects specific positions preferentially in a third gene. The data* looks ...
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1answer
31 views

Fisher's exact test in RNA-Seq

In RNA-Seq analysis it is common to use tests analogous to Fisher's exact test to evaluate whether a gene is differentially expressed in two measured conditions. Fisher's exact test relies on ...
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17 views

Combining FDR value acquired from different microarray probes

Dear all great helpers, First of all, I would like to note that I'm quite new in Microarray analysis, and I hope you all be patient with me. I would like to provide an example and ask you all a ...
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5 views

Representing pairs of proteins as feature vectors

I am attempting to predict whether two proteins will interact or not (binary classification task - pair of proteins as input and 1 or 0 for output indicating interaction). I have thousands of positive ...
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12 views

Best possible statistical approach to compare n pair of variables along a set of genomic intervals

I am dealing a bioinformatics problem and need help in approaching it in the right direction. I have a set of variables that represent different kinds of genomic data and are real valued. I am trying ...
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26 views

Discretizing count data (poisson distribution)

Hi I am using next generation sequencing data (Chip-seq) for a machine learning problem. The data is represented as counts of fixed sized regions of genome (in this case 1000 bp) each 1000 bp bin ...
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1answer
42 views

Working with subsets of the original data matrices for machine learning

I have seen very educational applications of pattern recognition on complete images. I was wondering if there are methods that could handle cases with the following specifications: instead of full ...
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47 views

How to predict with the known information in an undirected graph

Protein-protein interaction networks are known. It is an undirected graph. Each row of the networks is like this (Protein 2 - Protein 6), and It represents the interaction between Protein 2 and ...
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16 views

Are there any statistical fallacies that go with E-values?

I am presently learning how to use bioinformatics tools and among the first things to encounter was the notion of an E-value, explained on NCBI's help page for sequence alignment tool BLAST. As far as ...
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1answer
24 views

Biologically inspired ANNs

Does anyone know what kinds of pattern classifier artificial neural networks are more biologically inspired?
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11 views

Pair-wise analysis with large amounts of data

I was asked to do a pair-wise analysis with target genes(~60) vs. a large amount of expressed genes (~4200). Can anyone shed some light onto what the most efficent way to do this is? I was going to ...
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2answers
44 views

Testing predictive power of a set of features

This is perhaps a typical setup in Bioinformatics: we need to build a model to predict a dependent biological variable (say $y$), given a large set of (usually genomic) features $X$ (which might not ...
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37 views

How to use Chi Square test for Gene(feature) Selection in R?

I am following http://www.hindawi.com/journals/bmri/2014/589290/ article for chi square test for gene selection. According to this article all the gene expression of each sample will either be ...
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18 views

Validating poissonic (mutation) data using 95% confidence interval

I've been tasked with the following: We want to verify the quality of DNA sequences from a lab without redoing the assembly ourselves. These "query" sequences (say influenza) from the other lab are ...
2
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1answer
45 views

What statistics should I use to combine multiple rankings?

Problem: I have a list of genes and I am checking certain factors for each gene. I have individual scoring system for each factor for each gene. My final table/matrix looks like this: ...
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0answers
56 views

Adaptation of binomial testing: How-to?

My question arise from the field of genomics: Given that every chromosome exists in two copies, a specific feature can be present in 0 chromosomes (p=0) 1 chromosome (p=0.5) both chromosomes (p=1) ...
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11 views

Assigning score/values to a group based on its elements

I have three groups (group-A,group-B and group-C), each group contains elements with score/value for each element. For instance ...
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1answer
45 views

Advanced/Professional online data analysis courses [closed]

I've been looking for some statistics, data analysis or other connected with bioinformatics field online courses. Unfortunately, many of them have an introduction or beginner level (like on coursera) ...
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2answers
133 views

Comparing mutation frequency between a case and a pool of controls

I"m working in genomics and trying to come up with the appropriate statistical test for my question. To call mutations in a tumor's DNA, we use sequencing that samples from the total population of ...
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1answer
33 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
61 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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21 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
1k 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
105 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
108 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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0answers
40 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 ...
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1answer
125 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
115 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
41 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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1answer
61 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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102 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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50 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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31 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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1answer
27 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
109 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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93 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
115 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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2answers
125 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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17 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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105 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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42 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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68 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
258 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
234 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
55 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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237 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
85 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
27 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
294 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 ...