Showing : DifferentialExpression • reset
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 21 hours ago by 42k • written 1 day ago by • 0
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209
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 1 day ago by 50k • written 2 days ago by • 0
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7
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
8 days ago • updated 4 days ago sajadahmad41454 • 0
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 6 days ago by ★ 4.1k • written 6 days ago by • 0
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3
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 13 days ago by ★ 4.1k • written 14 days ago by • 0
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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 15 days ago by 65k • written 16 days ago by • 0
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6
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
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241
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 5 weeks ago by ▴ 30
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3
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277
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
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181
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
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3
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
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248
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
7 weeks ago Chanderkant Chaudhary • 0
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300
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 8 weeks ago by 42k • written 9 weeks ago by • 0
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3
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436
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
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4
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490
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
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4
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321
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago • updated 10 weeks ago mperalc • 0
2
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1
reply
317
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
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239
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
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2
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314
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
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6
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633
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
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3
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373
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
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3
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384
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
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13
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.1k • written 2.2 years ago by ▴ 30
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1
reply
231
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by ▴ 20
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2
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319
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by • 0
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5
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639
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
5
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6
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596
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
3
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1
reply
324
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
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4
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543
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 4 months ago by • 0
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3
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607
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
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3
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436
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
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1
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415
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
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371
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
1
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2
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450
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
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8
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1.6k
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Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 11 months ago by • 0
0
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1
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362
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 5 months ago by 42k • written 6 months ago by ▴ 10
1
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4
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575
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 6 months ago by 42k • written 6 months ago by ▴ 60
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8
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838
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
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384
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
7 months ago nromerov • 0
2
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6
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794
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
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4
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719
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
0
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434
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''Model_Matrix'' error
DifferentialExpression limma
updated 7 months ago by 50k • written 7 months ago by • 0
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587
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comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
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2
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533
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago Beyza • 0
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510
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Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
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408
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Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 8 months ago by 65k • written 8 months ago by • 0
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7
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3.0k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
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3
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585
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DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly? by ATpoint ★ 4.1k
High counts are generally less prone to noise compared to low counts. Bottom line is that you should stick to specialized testing framework…
Comment: Problem installing ChAMP on a MacBook by ATpoint ★ 4.1k
Did you run these lines? https://www.bioconductor.org/packages/release/bioc/html/ChAMP.html It is good practice to include code and error …
Comment: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 220
Looks like `sgv_pred` does not have the expected format. Was it created or edited manually? I would always recommend creating objects with …
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly? by pangtaihin • 0
Thank you:)
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly? by pangtaihin • 0
Thank you! But I apologize for cannot fully grasp your point. Do you mean that when the counts are high, rlogged matrix can represent the t…
Votes
Answer: Can DESeq2 rlog normalized matrix reflects time course result directly?
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
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