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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11 views

Training models for classification using different negative datasets

I'm working on a massively unbalanced binary classification task - Classification of given protein sequences as belonging to a certain (very small) class, or not. There are about 1,300 positive ...
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20 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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28 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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0answers
16 views

Selecting genes more affected in treatment A than treatment B

We are trying to test the hypothesis that a mild mutation of a gene has few effects on the expression of the transcriptome than complete deletion. Further we wish to test the hypothesis that the genes ...
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1answer
17 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
67 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
22 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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0answers
42 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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0answers
44 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
82 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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0answers
45 views

Estimating number of RNA-seq reads needed to detect differential expression

So I've spoken with two professors about this and I'm still confused. Maybe I need to see it in writing (I'm a visual learner). This is an experiment with Drosophila (fruit flies). Currently, our ...
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1answer
52 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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26 views

One experiment with many (dependent!) hypotheses for motif prediction in dna sequences

I am having the following problem. I have a group of words which are all permutations of each other. On a random dataset of DNA sequences I can calculate the distribution of the number of word ...
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2answers
36 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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0answers
19 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
141 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
220 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
175 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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0answers
27 views

Protein folding problem

I’m new to the field of protein folding problem. I’ve been searching and came across some books for predicting the structures (Introduction to Protein Structure Prediction: Methods and Algorithms). ...
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4answers
665 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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0answers
28 views

Binary classification of gene sequence data

I'm working on an older competition on Kaggle purely for self-study. The competition is to predict HIV progression given 2 nucleotide sequences, viral load (numeric), and CD4 count (numeric). The ...
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0answers
56 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
99 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 ...
5
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1answer
160 views

Binary classification of DNA motif sequences (bioinformatics)

I've been working on on a method for binary classification of DNA sequences. In more detail, here is what the method does. Given a family of DNA sequences, for example DNA sequence motifs, I try to ...
6
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1answer
81 views

Enrichment analysis by gene duplication level

Biological Background Over time, some plant species tend to duplicate their entire genomes, gaining an additional copy of each gene. Due to the instability of this setup, many of these genes are then ...
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1answer
49 views

Computing combinations [closed]

I am having a problem in getting all the combinations from my dataset. I need your suggestions and guidance in doing so. I have a file, whose first column contains the regions and other file five ...
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2answers
1k views

training approaches for highly-imbalanced data set

I have a highly-imbalanced test data set. The positive set consists of 100 cases while the negative set consists of 1500 cases. On the training side, I have a larger candidate pool: the positive ...
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2answers
289 views

Interpret Silhouette plot for large microarray dataset

For a microarray experiment with ~40,000 probes and ~30 samples I used the clara function from R to cluster my expression matrix. How do I interpret this silhouette plot? Firstly, I don't ...
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4answers
1k views

Framing the negative binomial distribution for DNA sequencing

The negative binomial distribution has become a popular model for count data (specifically the expected number of sequencing reads within a given region of the genome from a given experiment) in ...
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2answers
466 views

Learning Algorithms/Neural networks books? [duplicate]

Possible Duplicate: Machine learning cookbook / reference card / cheatsheet? Machine learning self-learning book? What are some good theoretical and practical machine learning algorithms ...
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1answer
596 views

How to calculate sensitivity, specificity, and odds ratio?

I am trying to calculate sensitivity, specificity, and odds ratio of a data set, they are numerical values of percentages from 0% to 100%. How should I do the calculation? Wikipedia has the formula: ...
5
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1answer
678 views

What is the advantage of median polish over the median?

I still can't figure out the advantage of median polish over a regular median for the summarisation of probe to make probesets in microarray analysis. As I understand from here the idea is to use the ...
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0answers
72 views

GWAS and Statistical theory - does the likelihood of a detectable main effect decrease with complexity?

I've been wondering recently about the difficulty of detecting statistically significant results from, say, genome-wide association studies. In these studies, many - ($10^{8}$) for example- ...
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0answers
88 views

How to give entire word a quality score to account for the phred score of each letter?

I have a word representing a DNA sequence and each letter of that word is a nucleotide base (A,T,G,C). Each letter has a phred quality score. The formula used for the phred quality score is ...
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2answers
181 views

How to calculate similarity in gene expression for each gene in two conditions and rank them?

I have expression values (log2) for 200 genes in two conditions treated and untreated and for each condition I have 20 replicates. The dataset looks like this: ...
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0answers
67 views

Unique subsequences of the human genome

I am working on a project involving genomes. I am going to divide a genome into subsequences, and then do something with those subsequences. I want to know if the subsequences that I produce are going ...
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3answers
2k views

What's the difference between statistics and informatics?

We always say that statistics is just dealing with data. But we also know that informatics is also getting knowledge from data analysis. For example, bioinformatics people can totally go without ...
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1answer
132 views

Estimating Diversity of operon types using HMMs across metagenomes: Mann-Whitney? Kruskal-Wallis? or other?

Question that seems complex but probably isn't. I'm comparing 10 metagenomes (http://en.wikipedia.org/wiki/Metagenomics), that are supposedly unrelated (they are 10 geographically separate ...
2
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1answer
281 views

Proposal for transition matrix for Metropolis-Hastings phylogenetic inference

I am using the Metropolis-Hastings algorithm for phylogenetic inference. To do so I would like to draw the substitution matrix Q from the generalized time-reversible model. To do so I need proposal ...
0
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1answer
150 views

Can clustering be used for log-odds scores?

I have data which looks like this. As you can see the data is symmetric and its not exactly a distance matrix. They are log odds ratios. And the diagonal values are higher than non-diagonal elements. ...
8
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1answer
266 views

DNA use in court cases

I am currently studying the following case of Neil Owen, based on the following article I found a newspaper: "A 20-year-old student was jailed for life yesterday for the brutal rape and murder ...
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0answers
216 views

P-value approximation from an underlying unknown distribution

I am calculating a certain statistic(relative entropy) of a certain sequence alignment over DNA sequences. The statistic has a certain distribution in the entire genome of which I only have 1000 ...
1
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1answer
332 views

Statistical tests for low sample numbers in both indendent groups (n=3 and n=1)

I've been asked to analyze some data for an experiment that's already been done. 15 rats were raised in 5 groups of 3 No treatment Saline treatment (control drug is delivered via saline) Drug ...
15
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3answers
1k views

Can the MIC algorithm for detecting non-linear correlations be explained intuitively ?

More recently, I read two articles. First one is about the history of the correlation and second is about the new method called Maximal Information Coefficient (MIC). I need your help regarding to ...
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0answers
144 views

Binary classification of DNA sequence motifs

[I apologize in advance for the length of this question. but it seems unavoidable.] I'm trying to do binary classification, using Bayesian methods, and I'm having some trouble figuring what methods I ...
4
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0answers
344 views

How to compare two power law distributions?

Disclaimer: I am a biologist, so please don't hesitate to correct me if I am making unwise assumptions. I am looking at the distribution of a unique 6mer in a series of 2100mer (I have 415 ...
1
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2answers
51 views

HMMs in protein or NA sequence alignments

I would be very grateful if someone could explain to me how hidden markov models are used to generate a sequence alignment. I was trying to read on it, however ended up in attaining basic concepts and ...
2
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0answers
85 views

Validating a model for a set of DNA sequences

Consider a set of DNA sequences i.e. strings composed from the four letters A, C, G, T. We model these sequences as a random vector, $\mathbf{X}=(X_1,\dots, X_n)$. Each member of the set of ...
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0answers
250 views

Problem with Bioconductor/limma on two-color factorial design: Coefficients not estimable

I'm running into a problem where my coefficients are not estimable when using Bioconductor/limma on a two-color factorial design for a microarray analysis. I have microarray data I downloaded from ...
9
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8answers
2k views

What are the “hot algorithms” for machine learning?

This is a naive question from someone starting to learn machine learning. I'm reading these days the book "Machine Learning: An algorithmic perspective" from Marsland. I find it useful as an ...