Questions tagged [bioinformatics]

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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parallel lines (cluster) in PCA plots (PC1 vs PC2)

There are about 20 subjects, 3 treatment groups, and 1000+ genes in my data; the 1000+ genes were processed in two batches. Could anyone comment on why I am seeing parallel lines/clusters in the PCA ...
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Number of variables to include in my GLM and how to interpret the surrogate value analysis

I am working with genes and I am designing a model that its dependent variable must be diagnosis, whereas the rest of potential variables to include are sex, ethnicity(2 levels), rin(RNA integrity ...
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4 votes
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Should I use a two-tailed t-test to generate p-values?

I have a data set similar to the one below. The real data set has 89 values in each column. I'm looking at the expression of RNA between two different treatments (treatment $X$ and treatment $Y$). <...
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Estimating Best Solution to Linear Equation

I believe this is quite a basic question, but want to make sure I'm doing this properly. I want to solve the following set of linear equations: $\text{RNA}_{1}=\text{RNA}_{Tumor}*\beta_{1}+\text{RNA}_{...
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How to provide the fold change value of a group of biological replicates?

I want to visualize relative gene expression with barplot + error bars after qPCR analysis. I was asked to use the log2FoldChange values for the barplots, where each bar should summarize 3 values (the ...
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I have to adjust p-value in One way ANOVA with 3 groups and 600 metabolites?

I have three groups: CC, CT and TT and 600 metabolites. When I do a lot of t-tests, I have to adjust the p-value, for example with fdr, but when I do a ANOVA with 3 groups, have I to adjust the ANOVA ...
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2 votes
1 answer
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A question for data scientists about Deep Learning Thesis [closed]

I am writing because I would like to ask more experienced people in Deep Learning about the (possible) topic of my master's thesis. I am not sure if it is not too complex and even possible to finish ...
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Can a heterogenous approach to data normalization yield a better consensus learning result?

The following makes sense intuitively, but I cannot find a reference: Let's say I've got 3 datasets, for example differential gene expression, of related experiments, where normalization was done in ...
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Should I use Raw Counts, TPMs, or RPKM gene expression values for training ML models?

I am currently using TPMs(Transcripts per Million) in my ML models, but I have read recently that this may introduce unwanted relations into the data. I know the raw counts are used to find ...
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1 vote
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What Statistical Test should I use to compare count data using two grouping variables?

My data represents the count of mutations by gene in two groups cases and ctrl. I would like to do comparison gene-wise between the two groups. But in my case I don’t think anova is appropriate since ...
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3 votes
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Linear mixed model (repeated measurements) on HUGE dataset

I have a huge dataset with measurements of 21k genes across 11k samples. The measurements, called expression, represent (roughly) how "active" that gene is in the cells of the sample (in ...
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Which type of Mixed Model is appropriate and which random effects to use with R lme()?

I have collected a data-set and run into some problems on how to correctly use a linear mixed model to analyse my data. The data collection (simplified): I have 24 family groups (“family”) of 2 ...
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2 votes
2 answers
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How to understand the formula:patient score = ∑PC1A−∑PC1B? [closed]

Today I read a paper (doi: 10.1016/j.omtn.2020.08.030), in this paper, they used many methods and finally they got a matrix, and each row represents a gene, each column represents a patient sample. ...
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What is a good approach to increase the depth of Nifti file format or Dicom file series?

I have a CT scan dataset of skull fracture consisting of multiple fractures and normal cases, the CT scans are in Dicom format. I want to do multi-class classification. But not every Dicom image ...
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Am I correctly implementing within-group correspondence analysis? (R)

I'm trying to conduct within-group correspondence analysis* on codon usage bias using R and I want to confirm I'm correctly using the ade4 package to do so. I have ...
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How to assess the difference between columns?

I have a data frame of enrichment scores for each sample with each gene signature. This is a study about a cancer drug. It has too many variables, this is a small chunk of it: ...
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1 answer
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Development of a sequencing-score (SeqScore)

I'm working with next generation sequencing on a daily basis and hence interpreting a lot of coverage analysis reports to decode the quality of sequencing runs. I'm using the Ion Torrent technology ...
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1 answer
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Normalization of test data when performing PCA projection

To briefly explain what I've been working on, I have two datasets: one as a reference(larger) and another for validation. I performed the PCA analysis with my reference dataset to create the ...
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What is the distribution of the number of reads that starts in a particular nucleotide in short read sequencing?

Short read sequencing is a high-throughput sequencing technology where a DNA molecule of $L$-nucleotides is broken down to and sequenced from small pieces ("reads"). The number of reads that ...
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Does negative transfer apply if coupled with auto-encoders?

I am reading a paper that applies transfer learning with an auto-encoder to de-noise genomic data, it is a fantastic idea and the paper is really interesting but I was thinking that surely aspects of ...
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How do I get the number of independent variables from a correlation matrix using R?

I have a correlation matrix for several thousand variables (gene expression in the form of a .bed file). Is there a way in R to use this to determine the number of independent variables in the dataset?...
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1 vote
0 answers
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statistical genomics resources [closed]

Does anyone have any good resources (books/papers/courses, etc) for statistical genomics/bioinformatics? I have no prior knowledge in biology, but I have a statistical background.
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CV% with Close-End Formula

I am working with qPCR data, where the quantity of genetic material (in picograms) is the direct output of the machine. The quantity is then entered into a close end formula, which accounts for ...
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Combining various annotation metrics to score genes?

A novice question. I want to score each gene based on the net score for a set of annotation variables in the columns. My aim for scoring the gene is gain an indication to the level of its impact/...
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1 vote
1 answer
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How to summarize multiple independent false discovery rates (FDRs or q-values)?

In the context of high-throughput biological assays (e.g. genomics), where we are applying a hypothesis test (e.g. differential expression between groups of samples) to each analyte in a dataset with ...
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1 vote
1 answer
445 views

How to properly display technical replicates in figures?

Let's say there was an experiment with two groups that I'd like to compare, both with three biological* (n = 3) and three technical* (N = 3) replicates each. For statistical analysis, I'd average the ...
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Determining a p-value for a test statistic that depends on other test statistics

Sorry for the confusing wording of the title. If some has any better way to word it, please feel free to change it. Background For those unfamiliar with bioinformatics data, I have data from a ...
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0 votes
1 answer
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Repeated measure with complex data structure

I have a set of age matched patients (40males and 40females). I am measuring the drug dose effect on their hormone outcome. They are treated for 4 weeks, each week we increase the drug dose starting ...
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2 answers
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How would I go about testing if there is any significant difference in the mean battery life between an Android phone and an iPhone?

Let's say that the following is the data for battery life in minutes for an Android phone: Android<-c(60,64,62,71,78,64,82,77,71,72,68,66,65,80,79,71,63,60,61) ...
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3 votes
1 answer
219 views

Cellular deconvolution intuition

Cellular deconvolution yields the proportion of cell types from bulk tissue. After estimating the proportion of each cell type, why cannot one multiply the total expression by the proportion to get ...
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1 vote
1 answer
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Analyses of Gene expression dataset, what stat test?

I was wondering if there was a way to analyse my RNA seq dataset in a way that I could work out which day the specific gene I have is most significantly expressed? I have a RNA seq dataset with 6 days ...
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1 answer
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Two Sample t-test with bootstrapping for gene expression matrix in R

I tried bioconductor packages for differential gene expression analysis such as EdgeR, Deseq2, Limma and obtained expressed genes by these methods. I want to compare my results with Two Sample t-test ...
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1 answer
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Validation on independent biological dataset

I am working in the space of cancer statistics. I am looking for reasons why it is important to validate statistical observations in an independent biological dataset. Does anyone have a list or a ...
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1 vote
1 answer
55 views

Cell colony survival mapping in a particular spatial pattern

I am attempting to spatially map the cell survival in a given scanned image of a cell flask. Quick background: the cells have received a high dose of irradiation (protons/X-rays) delivered through a ...
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1 vote
1 answer
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Given a graph, test if some vertices are more connected than the background

I have a neighborhood graph of some 10k vertices (a k-NN graph of single-cell RNA-seq data). I am interested if a given set of vertices is more connected to each other than you would expect by chance. ...
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211 views

Is this logistf approach the right way to deal with complete separation in my logistic regression?

I am performing lots of association tests between genotypes and binary diseases. The genotypes can be very rare, and my tests often have extreme case control imbalance (e.g. 500 controls for every ...
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1 answer
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Detrended canonical correspondence analysis in R

Is it possible to perform a Detrended Canonical Correspondence Analysis in R? Im looking to analyse ecological (pollen) data to investigate beta diversity through time. As far as I can tell I have to ...
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4 votes
3 answers
573 views

Is there a way to measure the degree of similarity between two columns?

I have a dataset of a list of genes with predicted scores (of likelihood to cause disease) from 2 different machine learning classifiers: ...
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1 vote
1 answer
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Is it possible to normalize features by one specific feature?

I have a dataset of genes with features that describe the genes at different scales (epigenetic, protein, cell, drug data etc. all numeric data). I use this dataset in supervised ML with a xgboost ...
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2 votes
1 answer
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Is it possible to use a feature as a mediator of other features in machine learning?

I have a dataset of genes with features that describe the genes at different scales (epigenetic, protein, cell, drug data etc. all numeric data). I use this dataset in supervised ML with a xgboost ...
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1 vote
2 answers
145 views

Differential gene expression using R

I am working on RNA Seq data analysis to get differential gene expression between 2 conditions. I am using ballgown package on R, and successfully loaded the data into R. However, I do have these ...
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1 vote
1 answer
44 views

Association between groups of features and outcome variable

I am working with a high-dimensional dataset (e.g., ~150 features) and possible confounders (e.g., ~10 features to control). The goal is to identify association with an outcome variable that is ...
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Statistically comparing two scatter plots in R

I have 2 different data sets (gene expression) where the same samples have been run on different platforms and the data has undergone different types of normalization. I have performed umap ...
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0 votes
1 answer
134 views

How to do ANOVA analysis for therapeutic biomarker screening for drug sensitivity

I am new to Bioinformatics. The graph below (from GDSC database) is to find therapeutic biomarker for drug sensitivity. I wonder how to do this kind of ANOVA analysis on my own so as to make this kind ...
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3 votes
0 answers
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How do I record randomly assigned data succinctly in a table

Please forgive me if I am posting this in the wrong forum. Here is the context of my question: I am conducting a drug trial, of sorts. I have 7-8 potential candidates for the treatment. Between ...
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1 answer
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How to choose a relevant threshold for HWE

I'm a beginner in biostatistics and GWAS study. For a quality control (pre-imputation), I need to perform a chi-square test on each SNP (there are 700 000 of them) to test the deviation for Hardy-...
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Problem with classification model of genomic data

First of all, I'd like to apologize for any spelling or grammar mistakes. I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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8 votes
1 answer
925 views

Best practices in the selection of distance metric and clustering methods for gene expression data

I have been reading about this on various channels including here and Stack Exchange, but I'm still not sure how to choose the best approach for clustering gene expression data. As a Ph.D. molecular ...
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R: Same dataset, different units and then, chi-square test no longer works

I am a beginner in R and statistics. I conducted Chi-square test to see if there is a significant difference/relationship between two distributions. Then, I changed my units to percentage over ...
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0 votes
1 answer
365 views

How to plot a heat map by giving scaling the color for row-wise?

I have a selected data table for DEG and interested in plotting a heatmap by using a color gradient row-wise (without scaling or normalizing the data). Giving a color key for the whole data set is ...
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