Showing : DifferentialExpression • reset
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
5 weeks ago Tadeoye ▴ 20
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9
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 6 weeks ago by 67k • written 7 weeks ago by • 0
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570
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 8 weeks ago by 52k • written 8 weeks ago by • 0
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466
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
9 weeks ago • updated 7 weeks ago abadgerw • 0
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5
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677
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
9 weeks ago • updated 6 weeks ago abadgerw • 0
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211
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
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6
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880
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 11 weeks ago by 43k • written 3 months ago by • 0
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3
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591
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 4 months ago by 52k • written 4 months ago by • 0
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3
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828
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
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3
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562
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 5 months ago by • 0
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5
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1.1k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
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3
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611
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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 5 months ago by ★ 4.6k • written 5 months ago by • 0
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5
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673
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 5 months ago by 67k • written 6 months ago by • 0
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460
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
6 months ago nhaus ▴ 70
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5
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1.9k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 6 months ago by • 0 • written 10 months ago by ▴ 50
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1
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473
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by ▴ 70
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4
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653
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
7 months ago vohara4 • 0
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1
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389
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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 7 months ago by 67k • written 7 months ago by • 0
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3
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449
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 8 months ago by 43k • written 8 months ago by • 0
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3
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690
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 8 months ago by 52k • written 8 months ago by • 0
0
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1
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405
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
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7
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1.2k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 months ago sajadahmad41454 • 0
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3
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861
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 8 months ago by ★ 4.6k • written 8 months ago by • 0
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3
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577
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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 8 months ago by 67k • written 8 months ago by • 0
0
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2
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543
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 9 months ago by 43k • written 9 months ago by ▴ 70
5
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6
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941
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 9 months ago by ★ 4.6k • written 9 months ago by ▴ 70
1
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3
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583
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 9 months ago by 67k • written 9 months ago by • 0
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2
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516
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 9 months ago by 67k • written 9 months ago by • 0
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2
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538
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
10 months ago • updated 9 months ago Chanderkant Chaudhary • 0
6
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5
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1.9k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 11 weeks ago by 52k • written 10 months ago by ▴ 50
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2
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595
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 10 months ago by 52k • written 10 months ago by • 0
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2
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749
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 10 months ago by 43k • written 10 months ago by • 0
1
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3
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754
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 months ago by • 0
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4
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708
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
10 months ago mperalc • 0
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0
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536
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
11 months ago Abril • 0
2
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1
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542
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
3
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2
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615
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 months ago Shaimaa Gamal • 0
4
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3
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773
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 months ago by 52k • written 11 months ago by • 0
2
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3
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719
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 months ago by 67k • written 11 months ago by • 0
2
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1
reply
480
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by ▴ 20
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2
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574
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by • 0
5
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6
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1.0k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 months ago Shaimaa Gamal • 0
4
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6
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1.1k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 months ago by 52k • written 12 months ago by • 0
3
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1
reply
616
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 12 months ago by 52k • written 12 months ago by • 0
1
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3
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951
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 13 months ago by • 0
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5
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1.1k
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Help with model for differential expression analysis
DifferentialExpression edgeR
12 months ago • updated 11 months ago Lucy ▴ 60
0
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3
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760
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
1
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1
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676
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 12 months ago by ★ 4.6k • written 12 months ago by • 0
2
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4
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910
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 12 months ago by 52k • written 13 months ago by • 0
0
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2
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784
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
13 months ago Luca • 0
50 results • Page 1 of 1
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Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Great thanks for posting the issue and sticking with it Annaleigh
Comment: Problems with oarfish + tximport + swish by brown.annaleigh • 0
Awesome possum! Update works!! Thank you so much for the help and guidance!
Comment: Postdoctoral Researcher in Spatial Gene Regulatory Networks underlying Stomatal by iqratechnology4 • 0
Iqra Technology is IT Solutions and Services Company. We are salesforce and Microsoft partner company. https://iqratechnology.com/
Comment: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt? by James W. MacDonald 67k
> BTW, shouldn't you be using keep.lib.sizes = F and re-do the calcNormFactors() after filtering of the dglst low-expression ENSGs, as Gord…
Comment: Problems with oarfish + tximport + swish by Michael Love 43k
Let me see if I can add some code to tximeta to cover this case. I've added an argument `skipRanges` in devel branch which should allow: …
Votes
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Answer: Limma Interaction Effect with Covariates
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