Questions tagged [differential-expression]

Use it when comparing a measure of the expression between two (or more) samples, where the units are relative to the comparison.

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Filtering criteria for non-coding features with very low counts

I am trying to do DE analysis of non-coding features of A. thaliana. I find in the miRNA and lncRNA counts file that they are abundant in zero counts, and most of the non-zero counts are very low. Now,...
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1 answer
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missing additional visits in GSE data

When downloading GSE data, often I encounter that the authors refer to additional visits in the data description, yet, they are not found in the data. For example, the following study. They mention ...
2 votes
1 answer
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Help with DIA-Mass Spectrometry data analysis with several conditions (limma?)

I am trying to learn how to analyse normalised DIA-MS data and I am struggling with it :// The original dataset I got is (6 conditions (2 samples each)) with 3 technical replicates (total: 36 sample ...
2 votes
1 answer
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Comparing multiple treatments to multiple other treatments in edgeR for simple effects in a complex experimental design

I am working with a RNA-seq data set in maize that has a relatively complex design. There are two levels of treatment A (nitrogen fertilizer level in the field, high or low), two levels of treatment B ...
1 vote
1 answer
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What statistical test to apply for DE after CibersortX deconvolution?

This question was also asked on Biostars I am running CibersortX in high-resolution mode (which yields estimates of gene values per sample). After that, I want to perform DE between two conditions on ...
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Q8 Accuracy Evaluation metric mathematical expression used in Protein Secondary Structure Prediction

I am working on Protein Secondary Structure Prediction using Recurrent Neural Network (GRU) model. I came across few open source projects which already worked on the similar problem. All of them are ...
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What method uses "diverge probability" in RNA-Seq differential expression analysis?

I am replicating differential expression analysis from a paper (here) on RNA-Seq data. I extracted the regulated genes using DESeq2::results with a threshold of 1 ...
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How to incorporate negative controls in DESeq2

We are doing a comparison between two outcomes (positive and negative). We could not have any positive controls as we do not have any "control" data to set as baseline, either from ...
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1 answer
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Would DESeq2 be appropriate or should I use another tool for differential gene expression?

Hay, this question is sort of an extension of previous post. We have sequenced extra cellular RNA from culture media. Since the number of cells were limited, we did not have enough material for ...
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1 answer
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Pathway Enrichment Analysis for one specific pathway?

I have a gene set containing a set of 1500 genes in which I did differential gene expression using limma voom pipeline. After this step I wanted to analyze a specific set of pathways the metabolism ...
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1 answer
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Can I perform Expression Analysis on this 10x dataset?

10x Genomics: 20k Human PBMCs is the dataset. Description of the dataset: Inputs/Libraries Human peripheral blood mononuclear cells (PBMCs) of a healthy male donor aged 30-35 were obtained by 10x ...
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Interpretation of clusterProfiler results

I am using clusterProfiler for differential gene expression using this code: https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html I have a question about the third line of code: <...
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Using PANDA to infer gene regulatory networks without ppi

I'm using this tutorial (https://github.com/netZoo/netZooM/blob/master/tutorials/panda/panda.pdf) to use PANDA to infer gene regulatory networks, but without ppi values (which I've been told can be ...
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1 answer
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What kind of data do I need to be able to complete Differential Expression using Limma

I am very new to bioinformatics but have some background in coding with R. I have been asked to find a data set and complete differential expression using the Limma package in R. I have tried a few ...
2 votes
2 answers
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Understanding DESeq2 output for resultNames

I'm following along with some pre written code to learn how to do differential expression. I am using the same data set and have gone back through the code and copy and pasted what they used and the ...
2 votes
1 answer
58 views

DE analysis tool and method for non-coding features

I am currently working with the non-coding features of A. thaliana, and trying to get the DE features. Among the three DE test methods in edgeR such as ...
3 votes
1 answer
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Issue with Differential Gene expression analysis with Deseq2

I am using the Deseq2 package to perform a DE analysis on multiple factors. So, basically to perform the analysis I consider patients characterized by the Brugada Syndrome type 1 and other patients ...
1 vote
1 answer
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Statistical methods suitable for DE analysis of non coding RNAs

I am currently working on DE analysis of coding as well as non-coding features of A. thaliana using the edgeR package. Is the negative binomial method that is ...
-1 votes
2 answers
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How do I calculate DEG cutoffs?

So for context, I have a set of TPM values for multiple genes for different samples, and I need to calculate the differential expression for RNA-seq values. I've been using this website as a guide: ...
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How to find the correlation between two genes and their separate overall survival outcome?

i am struggling to find the correlation between two isoforms and their survival outcome. i do have a dataset that is a cohort for thousands of genes and am only interesting in two which they should be ...
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How do I calculate differential expression for RNA-seq values with the "limma" package and the "ebayes" function?

So for context, I have a set of TPM values for multiple genes for different samples, and I need to calculate the differential expression for RNA-seq values. I've been using this website as a guide: ...
2 votes
2 answers
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RNAseq alignment: best practices for aligning to multiple isoforms?

I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions. Many of my (de novo assembled and ...
1 vote
1 answer
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To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass spect data using limma. Is there a way to make limma do the same ...
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What is the best approach to do a PCA analysis to distinguish between two groups?

I have two samples A and B and I do have an RNAseq for both of them. Inside each file (for A and B) I do have a set of FPKMs that give me a fold change for each gene (sample vs control). It looks ...
2 votes
1 answer
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Inconsistent replicate numbers in RNA-seq

I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control and treatment A and 3 replicates for treatment B (lost 2 replicates due to a mistake ...
0 votes
1 answer
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Different results in differential expression analysis of microarray data

I am performing differential gene expression analysis to microarray data for type 2 diabetes donors and nondiabetic donors. When I run the code I get some different results in each time (about 50 or ...
1 vote
1 answer
520 views

Differential gene expression: how do I correctly compare three groups to each other?

I'm trying to figure out the right way to do differential gene expression analysis with a discrete variable with three groups. The context is, I want to assess differential expression as a function of ...
0 votes
1 answer
109 views

Batch correction in differential expression analysis

I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company This is how my meta data look ...
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Manually calculating log2 fold change values from DESeq2 normalized counts [closed]

This question was also asked on Biostars and Bioconductor Support My aim is to perform gene clustering based on RNA seq datasets (raw expression values) from NCBI database. After clustering I realized ...
3 votes
2 answers
468 views

DESeq2 for large number of samples takes too much RAM

I am trying to run a very large number of transposase-accessible chromatin (ATAC)-seq samples through DESeq2 to find peaks of differential chromatin accessible across my study genome. I have about 100 ...
2 votes
2 answers
950 views

scRNA-Seq pseudobulk for marker detection

A standard approach for scRNA-Seq is to partition the single cells into individual clusters, then use a Wilcoxon test to find markers that characterize each cluster (or other statistical methods that ...
2 votes
1 answer
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Non-parametric, background-based tests on proteomics data from Proteome Discoverer v2.5?

I am new to proteomics analysis, so apologies if my question is silly! For context, I am working with proteome samples from the postmortem human brain for a case-control study. Our lab generally ...
0 votes
3 answers
146 views

Gene expression changes in one condition

I want to look at an RNA-seq data-set on 1 condition to look for expressed genes. As there is only one condition, I can’t perform differential analysis. The only thing I can think to do is set a ...
2 votes
2 answers
1k views

Differentially expressed genes analysis in Seurat

For the differentially expressed genes analysis, is it possible to check for DEGs based on the levels already identified in the object? For example, my dataset contains cells from 11 subjects, which ...
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Mass spectrometry: How to obtain expression counts for protein

I was given a data set consisting of 6 samples: 3 control and 3 treated. I dont have information about how data were generated and what the outputs represent. Each sample corresponds to a folder ...
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How to tune and use the MetaVolcanoR package

I conducted a differential expression analysis over several datasets, using LIMMA, each one on its own. For each dataset, I have a data frame of all the genes, with ...
3 votes
2 answers
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How should I interpret DGE results if only one HLA-A gene shows up as significant but not the others?

I have done a DGE recently and have been looking at the DGE list. One of the genes is HLA-A. However, when I dug deeper I realised there are hundreds of HLA-A genes with unique ENSEMBL number (of ...
2 votes
1 answer
592 views

What is the difference between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus for converting to gene symbols?

I am interested in the differences between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus. They yield the same results as seen in the code below. ...
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2 answers
868 views

Beginner with DESeq2 having issue with analysis

I am trying to run DESeq2 analysis on my featureCounts output counts table. I ran the following code: ...
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2 answers
105 views

Basic RNA Differential Expression in R

I have two matrices, one for individuals before treatment and one for the same individuals after treatment. Both matrices are raw read counts of RNA expression. ...
2 votes
2 answers
245 views

Comparing differential expression across samples - is batch effect correction needed?

I have a bulk RNA-seq dataset made up of control and treatment conditions for a range of cell lines. This dataset was generated in two batches, such that the cell lines are split between batches but ...
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4 answers
171 views

Where can I find Single Cell Data with Location "Coordinates"?

Does single cell data typically have the following meta-data: the "coordinates" (e.g. on a tissue, adjacent tissues) saying where each cell in the sample was located relative to other cells? ...
2 votes
1 answer
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RNAseq small sample size in control group

I am doing an RNAseq experiment with affected (n=6) and control groups (n=6) in cow. However it turned out that 4 of my control samples have very low quality so I have to discard them. My problem is ...
2 votes
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How can I separate upregulated genes from downregulated on a boxplot?

I have a table of fold change shifts for two different groups. Some of them are upregulated, others are downregulated. I wonder if it is ok to subset only positive values and to boxplot them to show ...
2 votes
1 answer
283 views

How to compare differential expression of same genes between two groups? [duplicate]

I need a statistically significant "decision" that DEGs from group A are different (or not) from group B (after drug treatment). For that, I have a mean fold change delta, calculated as the ...
1 vote
2 answers
128 views

What is the best way to compare differences in DEG expression between two populations?

I am interested in differential response to a drug in the "RED" group versus the "GRN" group. I mean, I need to compare differences in DEG expression between two populations (RED ...
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1 answer
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What is the best way to compare treated/control samples? [closed]

I have two populations of mice, say RED and GREEN; there are 5 pairs treatment/control in each. The table is the following: ...
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How can I get a column with real gene names in my ballgown analysis?

I am doing RNAseq analysis and I am using ballgown procedure for it. There is an option in R to calculate differentially expressed genes and use FPKM in calculating differential gene expression, which ...
-1 votes
1 answer
73 views

Visualizing top expressed genes

I have a spreadsheet of CPM values I want to visualize the top 20 genes expressed across my samples This is how my data look like ...
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The correct design for time series experiment

I have a treatment and control in two time points like this ...