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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15 views

How to calculate average EER and ROC?

If I test a system on 3 users and I obtain FARs and FRRs for thresholds and an EER for each user, how do I obtain an average EER and plot a ROC? As I see it, I could average the 3 EERs I have ...
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4 views

How to interpret the results of multcompLetters in R (clustering of groups using posthoc Tukey test results)

I am new to statistics and I am trying to conduct an analysis in R on data containing read count information for 45 samples. I carried out an ...
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1answer
13 views

RNA-seq: Controlling FDR in multiple contrasts

I'm working on a RNA-seq analysis project and I have come across a statistics problem. I have 3 groups and I need to look for differential expression for each pairwise comparison. Do I control the ...
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6 views

RNA-seq: Controlling FDR in multiple contrasts

I'm working on a RNA-seq analysis project and I have come across a statistics problem. I have 3 groups and I need to look for differential expression for each pairwise comparison. Do I control the ...
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21 views

In R, why is the survdiff function returning the p value = 0?

I want to obtain the pvalue of the three curves that are plotted. Here is the code that does a survdiff: ...
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20 views

Dealing with seeming outliers in microarray gene expression data

I have the following microarray gene expression data for one gene let us say. BTW - have similar data for the same subjects across 17000 genes, so I am looking for a generalized solution. ...
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30 views

How do I optimize a bioinformatics pipeline for novel data sets?

I'm putting the finishing touches on a bioinformatics pipeline for omics data. There are many sequential interlocking parts (e.g. model fitting, regression, classification, clustering, etc). The final ...
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20 views

Replicates handling in cross-validation

Currently, I try to analyze the gene expression data from approximately 1000 different samples, so I obtain a matrix of dimension 20000 (no. of genes) x 1000 (no. of samples), where each entry ...
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47 views

Statistical modeling of biomedical data in industry and hospitals: scopes and ways to do so

I hope my questions still follows the guidelines of this community. It's about my job-search. I'd like to know whether and how statistical modeling of biomedical data are in industrial or hospital ...
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27 views

How to preprocess the read count?

I am new to bioinformatics, and to learn more, I am starting by working on a project. I collected miRNA sequence data from the TCGA and it has a text file for each sample and the file includes: ...
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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 inactivated)...
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18 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
46 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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19 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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6 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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14 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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45 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 ...
2
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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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25 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
60 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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49 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 ...
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1answer
50 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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60 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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12 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
49 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
144 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
35 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 ...
4
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1answer
71 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
129 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
112 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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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 ...
2
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1answer
144 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 data....
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2answers
124 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
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
65 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
113 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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52 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
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
29 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
116 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 Benjamini-...
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0answers
105 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
125 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
130 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?