Showing : DifferentialExpression • reset
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
0
votes
8
replies
820
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago • updated 5 months ago Luca • 0
1
vote
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
2
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7
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2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
0
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6
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775
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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
5
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6
replies
547
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
4
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6
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594
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 12 weeks ago by 50k • written 3 months ago by • 0
5
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6
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423
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 days ago by ★ 4.1k • written 25 days ago by ▴ 30
2
votes
6
replies
969
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 10 months ago by 3.9k • written 11 months ago by • 0
2
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6
replies
772
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
0
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5
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612
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
2
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4
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514
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
0
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4
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298
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago mperalc • 0
1
vote
4
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551
views
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
votes
4
replies
743
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
3
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4
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424
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by ▴ 50
2
votes
4
replies
684
views
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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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
1
vote
3
replies
246
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 28 days ago by 65k • written 28 days ago by • 0
1
vote
3
replies
595
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
3
votes
3
replies
955
views
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
3
votes
3
replies
572
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
1
vote
3
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402
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
3
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567
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
4
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3
replies
351
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
0
votes
3
replies
110
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 2 days ago by ★ 4.1k • written 2 days ago by • 0
0
votes
3
replies
457
views
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
0
votes
3
replies
223
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 3 days ago by 65k • written 5 days ago by • 0
2
votes
3
replies
366
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
5
votes
3
replies
711
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
0
votes
3
replies
426
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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3
replies
647
views
limma paired design
DifferentialExpression limma
updated 10 months ago by 65k • written 10 months ago by • 0
0
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2
replies
745
views
DESeq: low p-values for genes with zero counts in all but one sample of the compared groups
DESeq2 DifferentialExpression
12 months ago António Miguel de Jesus Domingues ▴ 510
1
vote
2
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231
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
6 weeks ago • updated 5 weeks ago Chanderkant Chaudhary • 0
0
votes
2
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345
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
vote
2
replies
646
views
Obtention of the binomial transformed count table with edgeR
DESeq2 edgeR RNASeq DifferentialExpression
updated 12 months ago by 50k • written 12 months ago by • 0
0
votes
2
replies
682
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
1
vote
2
replies
415
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
0
votes
2
replies
165
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 29 days ago by 65k • written 29 days ago by • 0
0
votes
2
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320
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 7 weeks ago by 41k • written 7 weeks ago by • 0
1
vote
2
replies
528
views
Contrast of Contrasts in Limma
limma DifferentialExpression
12 months ago mpitz • 0
3
votes
2
replies
294
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
12 weeks ago Shaimaa Gamal • 0
0
votes
2
replies
517
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
0
votes
2
replies
295
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 41k • written 3 months ago by • 0
0
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2
replies
218
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 24 days ago by 41k • written 29 days ago by ▴ 30
0
votes
2
replies
281
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
1
vote
1
reply
530
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
1
reply
605
views
LIMMA: design with paired samples within and across treatments
DifferentialExpression limma
updated 11 months ago by 50k • written 11 months ago by • 0
2
votes
1
reply
296
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 11 weeks ago by ★ 4.1k • written 11 weeks ago by • 0
1
vote
1
reply
399
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
50 results • Page 1 of 1
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Replies
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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