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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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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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 ...
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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 ...
Mary Allen's user avatar
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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 ...
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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 ...
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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 ...
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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

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 ...
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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 ...
Shashank Nagaraja's user avatar
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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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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 ...
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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 ...
Programming Noob's user avatar
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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 ...
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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. ...
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Unclear variation in level 5 LINCS/L1000 gene perturbation Tx data and best practice to process

This question was also asked on Biostars I am trying to use level 5 gene KO/KD/OE & compound perturbation data (moderated z-scores for the 978 landmark genes) from LINCS L1000 (source: clue.io) to ...
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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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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 ...
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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 ...
Balint Biro's user avatar
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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 ...
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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 ...
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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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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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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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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 ...
Mark's user avatar
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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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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 ...
Exhausted's user avatar
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The correct design for time series experiment

I have a treatment and control in two time points like this ...
Exhausted's user avatar
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Understanding the different designs in DESeq2

I am using DEseq2 and trying to understand the results obtained using different models. I have a data design with 2 genotypes and 2 time points. ...
yathrakaaran's user avatar
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Different contrasts in DESeq2

I have a treatment and control in two time points like this ...
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Help with Limma-model

I'm starting to use Limma to find differential expressed sites within my data and would like to ask if my approach was correct. The data has a control and a treatment set, each containing data of 48 ...
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How to perform a meta-analysis using data consisting of paired-end and single-end reads generated from Illumina and Ion Torrent?

So basically I have RNA-seq reads that were generated from Illumina and Ion Torrent platforms for yeast species. I have seen an article where they compared liver cells of a rat that were sequenced ...
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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 ...
guest's user avatar
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Differential miRNA expression using RPM

I have microRNA (miRNA) expression data in RPM. I would like to do differential gene expression between two groups. How can I do this? I have considered edgeR and DESeq2 in R, but it looks like they ...
Sylvia Rodriguez's user avatar
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R limma alternatives in Python

The R package limma is ideal to perform differential expression analysis. Is there any limma alternative in Python? I'm trying ...
Gian Arauz's user avatar
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2 answers
312 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: ...
Justin1609's user avatar
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Seurat heatmap for two conditions

I have a Seurat object of four cancers and four controls ...
Mahta Mira's user avatar
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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 ...
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The biological meaning of the random variables and the responses in Seurat analysis

In the Seurat analysis, if we suppose that Xg and Xr denote the random variables that associate to the expression level of the gene g and of the gene r, respectively. Let Y and Yv represent the ...
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5 answers
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Normalize RNA seq data from multiple runs for expression analysis

I have RNA samples sequenced with TruSeq Stranded Total RNA kit protocol in Illumina HiSeq (2x125bp) and NovaSeq platforms (2x150bp) - almost 100 samples altogether. I have to use the samples data for ...
Praveen's user avatar
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Differential gene expression analysis of time series with replicates

I have a dataset that has two groups, perturbed vs control. Each group has 3 replicates. Each replicate has 8 time points. How do we do Differential gene expression analysis to find significantly ...
Hamda Binte Ajmal's user avatar
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Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases ...
jasperhyp's user avatar
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Clustering RNAseq fold-change data

I have a dataset that looks something like this Treatment1 Treatment 2 Control Sample1 3.23. 0.87. 1 Sample2 1.71. 1. 1 Sample3 2.88. 5.65 1 Sample4 0.77. 1.34 1 The numbers describe a fold ...
Anonymous Scientist's user avatar
1 vote
0 answers
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How to call this : some dots in volcano plot aligned a line after add a very small value to padj

when I plotting the volcano plot, I got some dots very top of the Y-axis because their padj nearly reached 0(I checked the data, I think they are reliable), so I followed the advice to add a very ...
Chu's user avatar
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Adding matrix as a confounder in EnrichmentBrowser

Brain data, particualrly human brain data have very heterogeneus cell types, so it's important to normalise by cell type/add proportoins of different cell types to the formula when performing ...
Sethzard's user avatar
1 vote
1 answer
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annotation using ChIPseeker package error

I have differential binding sites object obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error: Error in (function (classes, ...
Mariam's user avatar
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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? ...
gbrlrz017's user avatar
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Is there an established method for comparing expression of groups of genes (gene sets)?

I have a figure in a paper where I show the log2(fold-change) (obtained with DESeq2) between two groups (based on genotype) for genes within a specific hallmark gene set, and a reviewer is asking ...
Reilstein's user avatar
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Questions about EBSeq (in R)

I have made a UMAP of malignant cells and the result is split into 3 clusters, as seen below. For the sake of example, let's say I want to find the differentially expressed genes in the uppermost ...
tensor's user avatar
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Differential Gene Expression with Replicates for some of the samples

[this question has also been posted on Biostars; some additional clarification from there has been copied into this question] I've been asked to analyse a set of samples in which their control sample ...
Reza Rezaei's user avatar