Showing : DifferentialExpression • reset
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 9 days ago by 41k • written 13 days ago by ▴ 30
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6
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377
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 6 days ago by ★ 4.0k • written 9 days ago by ▴ 30
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220
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 13 days ago by 65k • written 13 days ago by • 0
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132
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 13 days ago by 65k • written 13 days ago by • 0
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196
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
28 days ago • updated 22 days ago Chanderkant Chaudhary • 0
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 22 days ago by 50k • written 29 days ago by ▴ 50
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2
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
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293
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 5 weeks ago by 41k • written 5 weeks ago by • 0
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3
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352
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
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4
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373
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by ▴ 50
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4
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262
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
7 weeks ago mperalc • 0
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191
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 weeks ago Abril • 0
2
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1
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274
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
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2
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259
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 weeks ago Shaimaa Gamal • 0
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3
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315
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
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3
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333
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
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1
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201
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 10 weeks ago by 41k • written 11 weeks ago by ▴ 20
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2
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267
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 11 weeks ago by 41k • written 11 weeks ago by • 0
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6
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515
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 weeks ago Shaimaa Gamal • 0
4
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6
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539
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
3
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1
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248
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
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3
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563
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 3 months ago by • 0
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5
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588
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Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 11 weeks ago Lucy ▴ 60
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3
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406
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
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1
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377
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
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4
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474
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
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2
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316
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
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2
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374
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
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1
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318
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by 41k • written 5 months ago by ▴ 10
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4
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523
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 5 months ago by 41k • written 5 months ago by ▴ 60
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8
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791
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
5 months ago Luca • 0
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341
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clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
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6
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745
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Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
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4
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642
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Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
6 months ago Shihui • 0
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1
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394
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''Model_Matrix'' error
DifferentialExpression limma
updated 6 months ago by 50k • written 6 months ago by • 0
3
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3
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556
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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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3
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439
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
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2
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486
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RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
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1
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487
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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 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
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1
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362
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Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 7 months ago by 65k • written 7 months ago by • 0
2
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7
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2.9k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 7 months ago by • 0 • written 3.0 years ago by ▴ 20
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3
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534
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DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 8 months ago by ★ 4.0k • written 8 months ago by ▴ 10
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427
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DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 8 months ago by 65k • written 8 months ago by • 0
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6
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749
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 8 months ago by 50k • written 9 months ago by • 0
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2
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661
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Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
1
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1
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512
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NA p values in edgeR results
DifferentialExpression edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
1
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8
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1.5k
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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 10 months ago by • 0
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3
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627
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limma paired design
DifferentialExpression limma
updated 10 months ago by 65k • written 10 months ago by • 0
0
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1
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489
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Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 10 months ago by 41k • written 10 months ago by • 0
1
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0
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452
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WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 10 months ago by 41k • written 10 months ago by ▴ 20
50 results • Page 1 of 1
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0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…
Comment: Finding DEGs by using edgeR by Gordon Smyth 50k
Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…
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