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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35 views

Beginner with DESeq2 having issue with analysis

Hi there I am brand new to using RStudio and trying to run DESeq2 analysis on my featureCounts output counts table. I ran the following code: ...
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Seurat heatmap for two conditions

I have a Seurat object of four cancers and four controls ...
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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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5answers
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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 ...
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1answer
42 views

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 ...
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36 views

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 ...
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How to perform KOG classification?

I have a list of DEGs and I want to perform KOG functional analysis, I try this method but WebMGA is not updated and seems to be deprecated. Are there any other online or standalone tools available ...
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42 views

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 ...
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How to merge several microarray-based gene expression datasets while not excluding genes that are not present in all datasets?

In integrative gene expression analysis when two expression matrices from different datasets are merged together, they are usually merged by common genes in both expression matrices while all other ...
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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 ...
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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 ...
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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, ...
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3answers
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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? ...
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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 ...
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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 ...
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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 ...
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a proper Design Matrix for several drug treatments with both control negative and control positive

I have a dataset of RNA-seq samples for testing different drugs on the presence of another drug. One of my samples is the normal cells with no drugs (control negative) and another is the cells with ...
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1answer
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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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Alternatives to imputation for single-cell RNA-Seq analysis to increase statistical power of DE analysis

I have a small scRNA-Seq dataset (n = 357, inhibitory neurons). This set of cells is split almost evenly between two conditions (Case and Control). I would like to test for differential expression ...
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2answers
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Separating peaks of chip-seq with specific length

My data contain several chip-seq results. I have the peaks called by MACS2.I wanted to only look at those peaks that their size is e.g 500bp to 1000bp. How can I separate those peaks efficiently? I ...
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1answer
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GSEA enrichr with 10x genomics differential_expression ranks

I am attempting to use GSEA enrichr with 10x genomics differential_expression rankings. Reading what people seem to be doing with GSEA, there seems to be a pre-/post-singlecell gene expression ...
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2answers
247 views

How to create a list of differentially expressed (DE) genes after normalization with RUVSeq?

I am using edgeR to perform differential expression (DE) analysis on a set of RNA-seq data samples (2 controls; 8 treatments). To correct for batch effects, I am using RUVSeq. I am able to get a list ...
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3answers
781 views

Is there an “official” standard usage of Red and Green on differential gene expression heatmaps?

I have recently found myself making multiple heatmaps for visualization of differential gene expression results between replicates in two experimental conditions. The default settings in the plotting ...
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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 ...
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What unit (TPM, FPKM/RPKM, or other) to use when working across samples

I have raw gene read counts and would like to perform an analysis across multiple samples. I've found conflicting info online on how this should be done. One commonality however is that FPKM/RPKM ...
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Is it conflicting: significant difference according to Wald test but not in PERMANOVA and ANOSIM to compare species abundances of metagenomic samples?

If there is no significant difference between two groups of metagenomic samples according to "Multivariate differential abundance tests" for example PERMANOVA and ANOSIM, does it makes sense to use "...
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Do I need to study alternative splicing and isoformswitch separately?

I have done a study on isoform switch between different tissue type. Now, many people asking me to study alternative splicing also. But, dont they will give me same results? If there is a significant ...
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DESeq2 compare within a condition

This might be a really stupid question, but I can't figure out how to do this. I've read through the DESeq2 vignette and manual pages but couldn't find an answer. I have a bunch of samples split up ...
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1answer
498 views

How to downsample some of the samples in RNA-seq data?

I have 40 samples and these are into two groups. I would like to perform a differential analysis between two groups. The library size of the samples is very low. But there are two samples (GroupA_12 ...
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1answer
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Differential Expression

I have genes differentially expressed between two groups (case and control). I would like to annotate them by classifying them according to their biological functions. I work on parasites of ...
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Filtering genes from cuffdiff results

This question has also been asked on Biostars I have run cuffdiff (with statistics turned ON) to compare two groups of samples: Control group and Late AD group. This is the command I ran to be precise:...
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How are these definitions related to differential expression?

I have two groups of patients; for each patient I have an output file (RNA-seq) contains this information ...
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STAR quantMode vs RSEM vs Kallisto

I recently discovered this Snakemake pipeline for RNASeq that uses STAR's quantMode to quantify gene expression for DESeq2 differential expression analysis. In the past I've always seen the workflow ...
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Differential gene expression bias due to effect of an individual sample

I am analysing a human single cell RNA seq experiment, where we have 4 groups, four samples each. Data has been analysed using Seurat, with the canonical workflow. I have tried DE using various ...
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777 views

Seurat define manually a cluster and find markers

I am aware of this question Manually define clusters in Seurat and determine marker genes that is similar but I couldn't make tit work for my use case. So I have a single cell experiments and the ...
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How I deal with this expression set?

I have a gene expression raw counts like below for 16 patients ...
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1answer
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How I deal with this kind of gene expression comparision

I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example tumor 1 in batch 1 and tumor 1 in batch 2 , ...
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1answer
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How to perform DE analysis for each sample

I am new to R and biocondunctor. I have the normalized expression values for 20 samples for a disease and for 10 controls. I wanted to get the differential expressed values for each sample with all 10 ...
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Identification of differential genes across 8 groups [closed]

I need to identify differential genes across 8 groups. I know this can be done using DESeq2 or EdgeR as these are better suited and equipped. However, I was thinking if something like this piece of ...
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Single sample in group: normal pipeline or Kal's Z test

As stated, which one is better for differential expression analysis? When I say normal pipeline I mean limma-voom, edgeR and DESeq2 pipeline for standard analysis. Kal's z test is mentioned in this ...
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2answers
461 views

Strange p-value histogram for differential gene expression analysis

I'm trying to perform pretty standard differential expression analysis using RNA-seq data. I've used Kallisto to perform RNA quantification and am using Sleuth to perform the differential expression ...
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1answer
606 views

Why does DESeq2 convert numeric columns to factor during differential expression analysis?

I'm attempting to perform differential expression analysis using DESeq2 on a dataset of ~90 samples and ~20000 transcripts. I have a number of variables I'd like to test against, some of which are ...
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Gene ratio as imput in limma

I have a data frame with gene-expression ratio. Is it possible to input this into limma/voom to find signinficannt gene-ratios between groups of samples? my data: ...
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1answer
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Merging transcriptomes coming from different experiments

I'm planning to build a transcriptome by pooling all existing transcriptomes in SRA for a non-model species (which has no reference genome) to study differentially expressed genes and the like. It ...
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1answer
279 views

load the phenotype data for ballgown

I am trying to reproduce the work of this paper [1], and I have run StringTie successfully, but after that I have to run Ballgown but could not understand this command: ...
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How to retrieve the best-scoring Trinity isoform from blastx results

I'm working on a somewhat unusual transcriptome focused on a killer X chromosome. This chromosome has some new genes, with expression levels quite different from their autosomal paralogs. I've found ...
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1answer
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I need some tips and suggestions for further analysis of NGS expression data (log2cpm)

I am a PhD student who inherited some log2cpm data of expression data from bulk kidney tissue from a UUO(unilateral urethral obstruction) experiment that tests a new drug. The sample material consists ...
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1answer
720 views

How to normalise scRNASeq data for differential expression analysis

I wish to perform differential expression analysis for cluster-specific gene expression in single-cell data (with a tool such as MAST or SCDE). I have data for 3 biological replicates. I performed ...
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What does an FDR value of 1 in RNA-seq mean?

I am looking at the supplemental data from the paper "An allelic series of miR-17 ∼ 92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron" which ...