Showing : differentialexpression • reset
2
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7
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2.9k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
0
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4
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737
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
1
vote
2
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402
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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
0
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2
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261
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
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6
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765
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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
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
9
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13
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6.5k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 12 weeks ago by ★ 4.1k • written 2.1 years ago by ▴ 30
1
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3
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387
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks ago by • 0
1
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3
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580
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
0
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8
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810
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago • updated 5 months ago Luca • 0
5
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6
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536
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
1
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4
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546
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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
0
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6
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767
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
1
reply
337
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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 41k • written 5 months ago by ▴ 10
2
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3
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358
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
0
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1
reply
495
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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
4
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3
replies
344
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
1
vote
3
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794
views
Is it okay to increase filtering to get more significant Adjusted P Values for DEGs found using Limma?
RNASeqPower edgeR DifferentialExpression limma RNASeq
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
1
reply
500
views
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
3
votes
3
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945
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Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by ▴ 20
0
votes
1
reply
408
views
''Model_Matrix'' error
DifferentialExpression limma
updated 7 months ago by 50k • written 7 months ago by • 0
1
vote
1
reply
395
views
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
0
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3
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638
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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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2
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152
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 25 days ago by 65k • written 25 days ago by • 0
0
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3
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453
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how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
1
vote
3
replies
238
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 25 days ago by 65k • written 25 days ago by • 0
0
votes
3
replies
417
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
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2
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309
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 6 weeks ago by 41k • written 7 weeks ago by • 0
1
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2
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525
views
Contrast of Contrasts in Limma
limma DifferentialExpression
11 months ago mpitz • 0
0
votes
1
reply
599
views
LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 11 months ago by 50k • written 11 months ago by • 0
0
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2
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743
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DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2 DifferentialExpression
11 months ago António Miguel de Jesus Domingues ▴ 510
3
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2
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285
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago Shaimaa Gamal • 0
1
vote
3
replies
557
views
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
0
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4
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1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
0
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5
replies
608
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
2
votes
1
reply
210
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 12 weeks ago by 41k • written 12 weeks ago by ▴ 20
5
votes
3
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700
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 4 weeks ago by 50k • written 5 weeks ago by ▴ 50
1
vote
2
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223
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 4 weeks ago Chanderkant Chaudhary • 0
0
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2
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337
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
vote
2
replies
639
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 11 months ago by 50k • written 11 months ago by • 0
0
votes
1
reply
379
views
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
0
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2
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673
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
3
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4
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413
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
4
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6
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571
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
0
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3
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169
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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 9 hours ago by 65k • written 1 day ago by • 0
0
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2
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289
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 41k • written 3 months ago by • 0
2
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4
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675
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
2
votes
1
reply
287
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 10 weeks ago by ★ 4.1k • written 10 weeks ago by • 0
0
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2
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206
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 21 days ago by 41k • written 25 days ago by ▴ 30
3
votes
3
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565
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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
50 results • Page 1 of 1
Recent ...
Replies
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
Votes
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
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