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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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Reasons for extremely low number of DESeq identified differentially expressed genes after RNAseq?

I am fairly new at RNA-sequencing analysis, but I have attempted to analyse the data I obtained from RNA sequencing on my own by following an online EdX class and by basing the majority of the ...
Adrianna V's user avatar
1 vote
1 answer
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time*treatment series with repeated (i.e: NOT independent) sampling of replicates

I am performing the analysis of cell cultures in suspension, untreated(U) and treatment A and B, at t0, t1 and t2, 4 replicates per treatment. The experiment started with 12 cultures, 4U, 4A and 4B, ...
Alfredo Pagliuca's user avatar
2 votes
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Memory issues in scrna_seq pseudobulk aggregation (for muscat Differential State Analysis)

I am new to working with scRNA-seq datasets and I keep running into memory issues when trying to perform differential expression analysis on my data. I know some memory trouble is to be expected with ...
Nora's user avatar
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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 ...
Kozolovska's user avatar
3 votes
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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 ...
Muhammad Usman's user avatar
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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 ...
Hadeer Ibrahiem's user avatar
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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 ...
Karthik Nair's user avatar
1 vote
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 ...
Karthik Nair's user avatar
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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 ...
Manuel Srgio Sokolov Ravasquei's user avatar
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1 answer
111 views

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: <...
Sylvia Rodriguez's user avatar
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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 ...
Feynman's user avatar
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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 ...
Sabrina's user avatar
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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 ...
Sabrina's user avatar
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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 ...
Alessia Avon's user avatar
2 votes
1 answer
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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 ...
Arkajyoti Banerjee's user avatar
1 vote
1 answer
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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,...
Arkajyoti Banerjee's user avatar
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 ...
Arkajyoti Banerjee's user avatar
-1 votes
2 answers
280 views

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: ...
Feynman's user avatar
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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: ...
Feynman's user avatar
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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 ...
Sam's user avatar
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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 ...
DavidR's user avatar
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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
1 vote
0 answers
48 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 ...
Lara's user avatar
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2 votes
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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 ...
Wang Ming's user avatar
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1 vote
1 answer
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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 ...
mrz123456's user avatar
0 votes
1 answer
125 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 ...
Zizogolu's user avatar
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1 vote
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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 ...
jayesh kumar's user avatar
3 votes
2 answers
581 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 ...
Shashank Nagaraja's user avatar
-1 votes
1 answer
88 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 ...
Antonio's user avatar
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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 ...
Kelly's user avatar
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1 vote
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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 ...
FalleS's user avatar
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1 vote
0 answers
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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
3 votes
2 answers
80 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 ...
Kento's user avatar
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1 vote
2 answers
107 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. ...
aurelius_37770's user avatar
2 votes
1 answer
708 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. ...
Nova's user avatar
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2 votes
2 answers
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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 ...
Alexlok's user avatar
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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 ...
Balint Biro's user avatar
2 votes
0 answers
92 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 ...
Mark's user avatar
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2 votes
1 answer
325 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 ...
Mark's user avatar
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1 vote
2 answers
137 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 ...
Mark's user avatar
  • 103
0 votes
1 answer
141 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: ...
Mark's user avatar
  • 103
2 votes
2 answers
257 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 ...
Bobbybobbobbo's user avatar
1 vote
0 answers
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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
  • 103
-1 votes
1 answer
83 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 ...
Zizogolu's user avatar
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0 votes
3 answers
154 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 ...
Zizogolu's user avatar
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1 vote
0 answers
49 views

The correct design for time series experiment

I have a treatment and control in two time points like this ...
Zizogolu's user avatar
  • 2,232
0 votes
1 answer
113 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. ...
yathrakaaran's user avatar
1 vote
1 answer
233 views

Different contrasts in DESeq2

I have a treatment and control in two time points like this ...
Zizogolu's user avatar
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3 votes
1 answer
195 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 ...
Lukas's user avatar
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0 votes
0 answers
72 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 ...
Justin1609's user avatar