Showing : DifferentialExpression • reset
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 20 hours ago by 51k • written 1 day ago by • 0
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163
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
12 days ago • updated 7 days ago abadgerw • 0
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270
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
12 days ago • updated 7 days ago abadgerw • 0
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1
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165
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 6 weeks ago by 42k • written 6 weeks ago by • 0
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6
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 26 days ago by 42k • written 6 weeks ago by • 0
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3
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513
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 3 months ago by 51k • written 3 months ago by • 0
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3
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654
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 3 months ago by 67k • written 3 months ago by • 0
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476
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 3 months ago by • 0
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5
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910
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
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3
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552
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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 4 months ago by ★ 4.5k • written 4 months ago by • 0
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5
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 4 months ago by 67k • written 4 months ago by • 0
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381
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
4 months ago nhaus ▴ 70
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5
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1.5k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 months ago by • 0 • written 8 months ago by ▴ 50
2
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424
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by ▴ 70
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575
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
5 months ago vohara4 • 0
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345
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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 5 months ago by 67k • written 5 months ago by • 0
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3
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397
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 6 months ago by 42k • written 6 months ago by • 0
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3
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615
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 months ago by 51k • written 6 months ago by • 0
0
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1
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373
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
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7
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1.0k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
6 months ago sajadahmad41454 • 0
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3
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732
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
0
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3
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516
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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 6 months ago by 67k • written 6 months ago by • 0
0
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2
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489
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 7 months ago by 42k • written 7 months ago by ▴ 70
5
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6
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848
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 7 months ago by ★ 4.5k • written 7 months ago by ▴ 70
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3
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542
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
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2
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427
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
1
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2
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485
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
8 months ago • updated 7 months ago Chanderkant Chaudhary • 0
6
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5
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1.7k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 22 days ago by 51k • written 8 months ago by ▴ 50
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560
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 months ago by 51k • written 8 months ago by • 0
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634
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 8 months ago by 42k • written 8 months ago by • 0
1
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3
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707
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 9 months ago by • 0
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4
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648
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 months ago mperalc • 0
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492
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 months ago Abril • 0
2
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1
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504
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 9 months ago by ★ 4.5k • written 9 months ago by • 0
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2
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566
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
9 months ago Shaimaa Gamal • 0
4
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3
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688
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 9 months ago by 51k • written 9 months ago by • 0
2
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3
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660
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 9 months ago by 67k • written 9 months ago by • 0
2
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1
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438
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 9 months ago by 42k • written 9 months ago by ▴ 20
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2
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535
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 9 months ago by 42k • written 9 months ago by • 0
5
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6
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955
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
10 months ago Shaimaa Gamal • 0
4
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6
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1.0k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 9 months ago by 51k • written 10 months ago by • 0
3
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1
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583
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 10 months ago by 51k • written 10 months ago by • 0
1
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3
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888
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 11 months ago by • 0
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5
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986
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Help with model for differential expression analysis
DifferentialExpression edgeR
10 months ago • updated 9 months ago Lucy ▴ 60
0
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3
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699
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 10 months ago by ★ 4.5k • written 11 months ago by • 0
1
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1
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628
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 11 months ago by ★ 4.5k • written 11 months ago by • 0
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4
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853
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 10 months ago by 51k • written 11 months ago by • 0
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2
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701
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
11 months ago Luca • 0
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2
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907
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 11 months ago by 51k • written 11 months ago by • 0
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1
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529
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 12 months ago by 42k • written 12 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Answer: HilBertVis install error by James W. MacDonald 67k
It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install `HilbertVis` on my work box…
Comment: Identical samples after deseq2 batch effect removal by maripane • 0
Thanks Michael for quick reply. Actually, I also questioned this but later i saw this issue happens within another cluster and different c…
Votes
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
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A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
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