Showing : DifferentialExpression • reset
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 5 months ago by • 0
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1
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1.3k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
6 months ago ktz • 0
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3
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928
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 months ago by 43k • written 8 months ago by • 0
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377
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 8 months ago by 43k • written 8 months ago by • 0
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523
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
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5
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676
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 9 months ago by • 0
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2
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678
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
10 months ago Tadeoye ▴ 20
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1.6k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 10 months ago by 68k • written 11 months ago by • 0
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3
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891
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 11 months ago by 53k • written 11 months ago by • 0
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824
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
11 months ago abadgerw • 0
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1.1k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
11 months ago abadgerw • 0
0
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1
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503
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
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6
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1.4k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 12 months ago by 43k • written 12 months ago by • 0
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3
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913
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 14 months ago by 53k • written 14 months ago by • 0
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3
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1.6k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 14 months ago by 68k • written 14 months ago by • 0
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3
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991
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 14 months ago by • 0
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5
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2.2k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 14 months ago by ★ 1.4k • written 14 months ago by • 0
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3
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958
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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5
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1.1k
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
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768
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
15 months ago nhaus ▴ 70
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5
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3.2k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 16 months ago by • 0 • written 20 months ago by ▴ 60
2
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1
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787
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 16 months ago by 68k • written 16 months ago by ▴ 70
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4
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1.1k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
16 months ago vohara4 • 0
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1
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627
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
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3
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758
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 17 months ago by 43k • written 17 months ago by • 0
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3
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1.0k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 17 months ago by 53k • written 17 months ago by • 0
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603
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
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7
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1.9k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
17 months ago sajadahmad41454 • 0
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3
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1.4k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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3
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883
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
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798
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 18 months ago by 43k • written 19 months ago by ▴ 70
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6
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1.4k
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by ▴ 70
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3
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869
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
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2
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977
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
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851
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
19 months ago Chanderkant Chaudhary • 0
8
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5
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3.2k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 months ago by 53k • written 19 months ago by ▴ 60
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2
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840
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 19 months ago by 53k • written 19 months ago by • 0
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2
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1.1k
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 19 months ago by 43k • written 19 months ago by • 0
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3
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994
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 21 months ago by • 0
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4
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990
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
20 months ago mperalc • 0
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742
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
20 months ago Abril • 0
2
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1
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775
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
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2
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968
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
21 months ago • updated 20 months ago Shaimaa Gamal • 0
4
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3
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1.1k
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 21 months ago by 53k • written 21 months ago by • 0
2
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3
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1.1k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 21 months ago by 68k • written 21 months ago by • 0
2
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1
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715
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by ▴ 20
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2
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821
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by • 0
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6
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1.5k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
21 months ago Shaimaa Gamal • 0
4
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6
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1.6k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 21 months ago by 53k • written 21 months ago by • 0
198 results • Page 1 of 4
Recent ...
Replies
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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