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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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
34 views
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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42 views
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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35 views
How could I find Differential Genes in Expression Matrix File by R?
I tried to get gset of my dataset by getGEO function, but unfortunately it didn't work( I installed GEOquery package) and i get errors like this:
Found 1 file(s)
GSE69606_series_matrix.txt.gz
trying ...
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1answer
20 views
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
100 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 ...
0
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1answer
37 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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40 views
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:
...
3
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1answer
71 views
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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68 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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0answers
20 views
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
54 views
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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32 views
Common Mouse and human DEG analysis
I have DEGs from human and mouse (equivalent of a human disease model), and would like to generate a logCPM correlation plot between the overlapping mouse and human gene (275 genes). Prior to ...
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1answer
225 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 ...
5
votes
2answers
418 views
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 ...
1
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1answer
199 views
Compare clusters from different datasets
I have two scRNAseq datasets, and I select a cluster from one of them, and another cluster from the other. I want to find differentially expressed genes between the ...
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1answer
171 views
DESeq2 complicated design - effect of replicated samples
I have RNAseq data from a relatively complicated experimental design with variables = genotype, treatment, time, and batch. I have 2 biological replicates for each genotype/condition, however ...
3
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1answer
88 views
Change sample names while using cummeRbund
I want to analyze RNA seq data using R package cummeRbund. Using this package I have a problem changing sample names. When I run this command in cummeRbund
...
2
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3answers
131 views
Selection of differential expressed genes
I'm working with RNA-seq data. I have 40 tumor samples and 5 Normal samples. Differential analysis with Deseq2 based on Fold change > 1.2 and alpha < 0.05 gave ...
4
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1answer
73 views
Is removing samples based on clustering for downstream analysis a right choice?
I'm using TCGA Lung cancer data. I'm interested in doing differential analysis between Lung vs Normal. Before DEA, to check the distance between each pair of samples I plotted an MDS plot:
In this, I ...
3
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1answer
77 views
Detecting differentially expressed genes with foldchange >= 2 and FDR < 0.05
I'm using edgeR for differential analysis. Using glmTreat function I'm detecting differentially expressed genes between Tumor and Normal. I have set the arguments like below:
...
2
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2answers
39 views
Can I ask DESeq2 which variable alone explains which gene's behavior the best?
Imagine I have a dataset of highly periodic gene expression, taken at densely spaced timepoints. I know that the expression is periodic, but different genes have different offsets.
It is trivial to ...
5
votes
2answers
91 views
Smallest group size for differential expression in limma (bulk RNA-Seq)
I am reading Smyth et al. (ref. 1). I want to run differential expression analysis on a bulk RNA-Seq dataset in which each group is composed by 2 samples. In the paper previously cited it is written ...
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3answers
188 views
Expression of a gene in different groups
I would like to check the expression of a gene in different groups like Disease vs Normal samples. I want to make a plot out of that to check whether it is significant or not.
From this paper lncRNA ...
3
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2answers
84 views
What kind of analysis can be done with differential expression of transcription factors?
I have two different stem cell types and their respective gene expressions from RNAseq.
I noticed that there is differential expression in some of the genes coding for histones as well as ...
2
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1answer
702 views
Performing t.test to obtain p.values for each gene
I have FPKM values for Normal(80 cases), Group1(135 cases), Group2(147 cases), and Group3(102 cases) for 160 genes (Groups were obtained by clustering tumor data).
I want to perform t-test (two-...
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1answer
64 views
How to calculate call detection values in microarray datase if .cel file unavailable
I would like to do a differential gene expression analysis on a microarray data. From the literature, I understood, call detection (Present, Absent, Marginal) has to be done to minimize false ...
2
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0answers
472 views
Which R package to use for differential analysis with TPM values?
I'm using hisat2, stringtie tools for the RNA-Seq analysis. After stringtie using ballgown I get FPKM and TPM values for every gene.
I have seen that edgeR, Deseq2 can be used for Counts data. I ...
5
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1answer
166 views
Which tools for differential expression analysis in scRNA-Seq?
I am starting to run analysis for differential expression in scRNA-Seq. Which tools are available for this kind of analysis?
Can tools for bulk RNA-Seq like DESeq be used for scRNA-Seq?
5
votes
1answer
76 views
Can I use DRIMseq to model interaction effect of variables?
I am trying to use DRIMseq for DTU with 2 treatments on two different strains of mice. In my previous analysis with genes only, I had found a strong interaction effect of strain and treatments. Is it ...
8
votes
1answer
286 views
Comparison of gene set enrichment statistics
I am performing a gene set enrichment analysis to determine if particular gene sets are coherently up- or down-regulated. I have seen several statistics for computing a p-value of GSEA-style ...
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1answer
61 views
differential expression multiple studies
I was wondering if we can perform differential expression on samples from different library and read lengths.
What we intend to do is,
n = 6 tumors (recently sequenced using Hiseq 2500 read length ...
2
votes
1answer
105 views
Why do I obtain very strange results with DESeq2?
I am using DESeq2 to perform a differential expression analysis, but I obtained very strange results for some genes. For some genes, I have very high log2FoldChange with very low p-value as displayed ...
5
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1answer
98 views
How can I specify to DEseq2 to only perform comparisons on which I am interested with?
I am currently performing a large RNA-seq analysis from mice PBMCs. The dataset contains around 6,000 transcriptomic profiles and I would like to use DESeq2 to identify the sets of differentially ...
2
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1answer
32 views
Simple Affy Differential Expression
I think I have a fairly easy-to-solve problem.
I have an expression table generated from an Affy set. It has one row of gene names (already symbols) and then 180 sample rows. 181 rows total.
So I ...
5
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2answers
70 views
Differential Expression With 2 Treatments
I have a expression data from a small cohort of samples taken at baseline and after 2 independent treatments. I can do differential expression contrasting T1 and T2 or I can contrast T1 vs baseline ...
3
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1answer
118 views
error in heatmap using R
I am learning about generating heatmaps using R. For this example I am using randomly generated data to test the process, but I encountered what appears to be an error or perhaps there is something am ...
4
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1answer
64 views
Standard Cutoff for Moderated T-statistics
I'm looking at some microarray data. For the first time I've calculated a moderated T statistic from limma.
Is there any standard practice for where to cut off that value? For log2 fold change I ...
3
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3answers
471 views
Error in creating a volcano plot in MATLAB
I am a complete newbie to MATLAB and the first task I have is to create a volcano plot. I have been using this link to understand about it and get started.
I tried to run it on dummy values -
...
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2answers
254 views
Correct for gene length or read counts in GO enrichment analysis
It is a well reported fact that GO analysis of RNAseq results is affected by a number of biases, including length bias and expression level bias.
The bioconductor ...
4
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1answer
68 views
Using signal peptide and the expression levels of signal recognition particle in secretome analysis
I have not found any work which investigates assessment of differences in levels of secreted proteins by taking advantage of differential expression of the genes which mediate the secretory pathway.
...
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2answers
63 views
Can gene co-expression networks be used to help identify differentially expressed genes?
In my RNAseq dataset of differentiated stem-cell lines, some samples have far fewer significantly differentially expressed genes than others. QC shows that this is because there are way fewer reads ...
8
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1answer
335 views
Sleuth: transcripts with beta close to 0 are considered differentially expressed in a likelihood-ratio test
I'm comparing the results that I obtain when doing a DE analysis with the Wald test and the likelihood-ratio test. One the thing that I've noticed is that there are many genes with 'beta' close to ...
6
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3answers
2k views
Removing PCR duplicates in RNA-seq Analysis
After reading some of the forum posts in Biostar and SeqAnswers I find it very confusing whether to filter out the duplicate reads from aligned files or not. As far I understand it's very difficult to ...
7
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2answers
311 views
differential gene expression complex design no replicates
We have an experimental design as seen below
Where we administered drug at 0 min for each mouse genotype and took them down at given below intervals. wt and ko mouse models were administered only ...
6
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2answers
505 views
Running differential expression analyses on count matrices with many zeroes
Note: I also posted this issue (with less context) in the bioconductor support site: https://support.bioconductor.org/p/97424/
I'm working on a snakemake workflow that identifies various small RNA ...
7
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2answers
638 views
Getting a “system is computationally singular” error in sleuth
I am analysing 142 samples belonging to 6 batches. Additionally, those samples belong to 72 strains, which means that for most of the strains there are two samples.
I could fit simple models (for ...
6
votes
2answers
321 views
Searching for gene expression data by cell line
I have two cancer cell lines (OCI-Ly18 & riva) that I want to find gene expression data for, but I'm not aware of many gene expression databases that allow searching by cell-line without searching ...
6
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2answers
381 views
Missing genes and normalisation of RSEM output using EBSeq
Without going into too much background, I just joined up with a lab as a bioinformatics intern while I'm completing my masters degree in the field. The lab has data from an RNA-seq they outsourced, ...
6
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1answer
69 views
Gene set enrichment analysis on differential phosphorylation sites
I have:
A list of differentially phosphorylated sites in a knockout condition. Some genes contain as many as 70 possible phosphorylation sites; others contain only one.
A list of genes belonging to a ...
