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.
119
questions
1
vote
1
answer
60
views
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 ...
- 177
2
votes
2
answers
41
views
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 ...
- 23
1
vote
1
answer
52
views
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 ...
- 11
1
vote
0
answers
40
views
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 ...
- 21
2
votes
1
answer
29
views
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 ...
- 101
1
vote
1
answer
82
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 ...
- 11
0
votes
1
answer
70
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
...
- 1,791
1
vote
0
answers
386
views
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 ...
- 51
3
votes
2
answers
193
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 ...
1
vote
1
answer
69
views
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 ...
- 141
2
votes
1
answer
83
views
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 ...
- 21
1
vote
0
answers
19
views
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 ...
- 11
1
vote
0
answers
35
views
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 ...
- 169
3
votes
2
answers
75
views
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 ...
- 67
1
vote
2
answers
96
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.
...
0
votes
0
answers
19
views
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 ...
- 13
2
votes
1
answer
255
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.
...
- 165
2
votes
2
answers
443
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 ...
- 277
2
votes
1
answer
60
views
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 ...
- 75
2
votes
0
answers
79
views
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 ...
- 103
2
votes
1
answer
65
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 ...
- 103
1
vote
2
answers
87
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 ...
- 103
0
votes
1
answer
75
views
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:
...
- 103
2
votes
2
answers
153
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 ...
1
vote
0
answers
62
views
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 ...
- 103
-1
votes
1
answer
55
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
...
- 1,791
0
votes
3
answers
103
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 ...
- 1,791
1
vote
0
answers
39
views
The correct design for time series experiment
I have a treatment and control in two time points like this
...
- 1,791
0
votes
1
answer
69
views
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.
...
1
vote
1
answer
194
views
3
votes
1
answer
121
views
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 ...
- 33
0
votes
0
answers
54
views
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 ...
- 41
0
votes
1
answer
82
views
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
0
votes
0
answers
144
views
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 ...
- 205
3
votes
1
answer
2k
views
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 ...
- 151
0
votes
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:
...
- 41
0
votes
1
answer
1k
views
1
vote
1
answer
100
views
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 ...
- 11
1
vote
1
answer
57
views
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 ...
- 163
1
vote
5
answers
507
views
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 ...
- 11
1
vote
1
answer
182
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 ...
1
vote
1
answer
41
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 ...
- 13
0
votes
1
answer
262
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 ...
1
vote
0
answers
48
views
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 ...
- 13
0
votes
0
answers
56
views
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 ...
- 95
1
vote
1
answer
410
views
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, ...
- 95
0
votes
4
answers
150
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? ...
0
votes
1
answer
131
views
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 ...
- 367
1
vote
0
answers
21
views
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 ...
- 11
1
vote
0
answers
189
views
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 ...
- 169