Tagged Questions

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

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
9 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
10 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
15 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
25 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
12 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
68 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
12 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
43 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
16 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
14 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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0answers
29 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
51 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
53 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
9 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
49 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
15 views

Significance of the distribution of DNA sequences given a certain nucleotide bias

I have a large sequence of DNA in which every position can have 4 different states, or nucleotides (A,T, G or C). The distribution of the nucleotides in the sequence is non-random and, most ...
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0answers
23 views

Sample size question - ill posed question?

I'm working on a project in which we are performing clustering on high dimensional data (~1000 variables) and looking for subpopulations of observations that result from clustering. Think gene ...
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0answers
38 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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0answers
86 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
59 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
22 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
20 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
111 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
32 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
47 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
58 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
108 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
80 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
55 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
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1answer
29 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
247 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
264 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
225 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 ...
1
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4answers
2k 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. ...
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1answer
122 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
189 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
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1answer
89 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
67 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
2k 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 ...
0
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2answers
371 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 ...
13
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4answers
2k 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 ...
0
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2answers
809 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 ...
-1
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1answer
680 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
votes
1answer
867 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 ...
1
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0answers
87 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
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0answers
103 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
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2answers
213 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: ...
0
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0answers
73 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 ...