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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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1answer
77 views

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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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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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 ...
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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: ...
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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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0answers
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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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
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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: ...
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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 ...
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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 ...
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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 ...
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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 ...
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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
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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
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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
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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
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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 ...