The bioinformatics tag has no wiki summary.
15
votes
3answers
3k views
Extending the birthday paradox to more than 2 people
In the traditional birthday paradox the question is "what are the chances that two or more people in a group of n people share a birthday". I'm stuck on a problem which is an extension of this.
...
14
votes
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 ...
11
votes
4answers
768 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 ...
9
votes
7answers
432 views
Making sense out of statistics theory and applications
I have recently graduated with my masters degree on medical and biological modeling, accompanied with engineering mathematics as a background. Even though my education program included a significant ...
8
votes
1answer
223 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 ...
7
votes
7answers
947 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 ...
7
votes
3answers
585 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 ...
5
votes
3answers
2k views
Calculating False Acceptance Rate for a Gaussian Distribution of scores
I have a biometric system that outputs a distribution of scores that resembles a Gaussian distribution (similar to the example graph in the following link: LINK). My point of confusion is how I ...
5
votes
1answer
431 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 ...
5
votes
1answer
120 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 ...
4
votes
3answers
2k views
Calculating the probability of gene list overlap between an RNA seq and a ChIP-chip data set
Hopefully someone on these forums can help me out with this basic problem in gene expression studies.
I did deep sequencing of an experimental and a control tissue. I then obtained fold enrichment ...
4
votes
1answer
45 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 ...
3
votes
2answers
157 views
Efficient Empirical CDF Computation / Storage
I'm trying to precompute the distributions of several random variables. In particular, these random variables are the results of functions evaluated at locations in a genome, so there will be on the ...
3
votes
2answers
253 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 ...
2
votes
1answer
416 views
Clustering large and sparse datasets
I have a few datasets of "interactions" between pairs of elements like so:
...
2
votes
1answer
61 views
Analysis of variables of varying numbers
I work with amino acid sequences and I want to use a self-made model to tell me something about it, lets call it $f(\text{seq})$. Now i want to know the contribution of every position in the sequence ...
2
votes
0answers
131 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 ...
2
votes
0answers
232 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 ...
2
votes
0answers
78 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 ...
1
vote
1answer
145 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 ...
1
vote
2answers
130 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:
...
1
vote
1answer
57 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 ...
1
vote
1answer
115 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 ...
1
vote
2answers
48 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 ...
1
vote
1answer
134 views
Demo for bioinformatics
I am a beginner level programmer preparing for the interview in medical research company. Job sounds damn interesting and I would like to get there.
To show my skills and interest, I want to write a ...
1
vote
0answers
58 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- ...
1
vote
0answers
73 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 ...
1
vote
1answer
178 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 ...
1
vote
0answers
113 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 ...
1
vote
0answers
161 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 ...
1
vote
1answer
76 views
Ordered sampling of uniform variables
I need to sample starting positions in a DNA sequence of given length L.
These starting positions represent starting points of functional domains in DNA sequences. They have a length of d. The ...
1
vote
0answers
226 views
Interpretation of 3-way ANOVA
I have 2 genes (tf1 and tf2), which are affecting a third gene (tg). By affecting a gene I mean the changes in the value of tf1 and tf2 changes the value of tg. what we measure in the whole experiment ...
1
vote
0answers
195 views
Assessing DNA sequencing quality
I work with a lot of bar charts. In particular, these bar charts are of basecalls along segments on the human genome. Each point along the x-axis is one of the four nitrogenous bases(A,C,T,G) that ...
0
votes
2answers
206 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 ...
0
votes
2answers
208 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 ...
0
votes
1answer
37 views
Computing combinations
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 ...
0
votes
1answer
119 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.
...
0
votes
1answer
44 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 this two groups with some statistical test. ...
0
votes
0answers
20 views
Comparison of gene expression of 2 groups with only 1 individual each
I have expression level data of 19 genes of 2 individuals, one with a treatment and other without treatment. Duplicates measures are done for each gene.
The procedure is very expensive and it is not ...
0
votes
0answers
74 views
Is it possible to use Mic (maximal information coefficient) as an 'evolution' of partial correlation?
I have seen on a 11 months ago question here the following quote from a paper referred on the question:
...
0
votes
0answers
289 views
Bioinformatics's svmtrain using MLP Kernel Function
I am using Bioinformatics's svmtrain, with mlp kernel function for classification. However, I encountered an error when using quadratic programming 'QP' to train.
As recommended in the documentation, ...
0
votes
0answers
61 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 ...
0
votes
0answers
31 views
A measure to identify discriminating subgraphs of a larger graph?
I have genes from four species of bacteria. I constructed an undirected graph from the sequence similarity between all the genes from these bacteria. Each node in the graph is a gene and each edge is ...
0
votes
0answers
181 views
What's the difference between 18S rRNA and 18S rDNA? [closed]
Perhaps this question is a bit borderline for this site (although I'm hoping it's a reasonable question for someone specialising in bioinformatics).
I'm after a straightforward explanation of the ...
-1
votes
1answer
453 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:
...
