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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23 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
28 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 ...
0
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2answers
29 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 ...
2
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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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0answers
36 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 ...
1
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1answer
27 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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0answers
45 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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0answers
37 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
23 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 ...
0
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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
13 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 ...
0
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1answer
42 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 ...
0
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0answers
18 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
14 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
50 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 ...
1
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0answers
60 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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0answers
14 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 ...
0
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2answers
92 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 ...
1
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0answers
14 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
61 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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0answers
28 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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0answers
24 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 ...
0
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0answers
35 views

Estimation of Noise Level in the High-Throughput Cancer Data

Assume that I have made a coverage log ratios signal by dividing the coverage data coming from a tumour sample over the reference sample and then taking the log2 of this division. My question is: ...
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1answer
113 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 ...
1
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1answer
117 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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0answers
17 views

Modelling biases in selection of one choice from many using count data

In a biological experiment I draw somewhere between 100k and several million datapoints, where each datapoint is one of 1024 DNA sequences. If each sequence has an equal probability of coming up, I ...
1
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1answer
50 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
137 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 ...
0
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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 ...
1
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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
156 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
35 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 ...
0
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0answers
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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0answers
68 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
112 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
113 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
73 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 ...
1
vote
1answer
33 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 ...
1
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1answer
361 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
votes
1answer
314 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
votes
2answers
299 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 ...
0
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0answers
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. ...
1
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1answer
133 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
votes
1answer
216 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 ...
7
votes
1answer
101 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 ...
0
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1answer
88 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 ...
7
votes
2answers
4k 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 ...