Showing : differentialexpression • reset
9
votes
13
replies
6.5k
views
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
vote
8
replies
1.5k
views
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
0
votes
8
replies
810
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago • updated 5 months ago Luca • 0
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
0
votes
6
replies
768
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
2
votes
6
replies
765
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
5
votes
6
replies
538
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
4
votes
6
replies
572
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 weeks ago by 50k • written 3 months ago by • 0
5
votes
6
replies
411
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 17 days ago by ★ 4.1k • written 21 days ago by ▴ 30
2
votes
6
replies
958
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 10 months ago by 3.8k • written 11 months ago by • 0
0
votes
5
replies
608
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
0
votes
4
replies
737
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
2
votes
4
replies
502
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
0
votes
4
replies
1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
11 months ago ruba-mahmoud • 0
0
votes
4
replies
287
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
9 weeks ago • updated 8 weeks ago mperalc • 0
3
votes
4
replies
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
2
votes
4
replies
675
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
1
vote
4
replies
546
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
3
replies
454
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
1
vote
3
replies
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
1
vote
3
replies
581
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 4 months ago by • 0
3
votes
3
replies
946
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
5
votes
3
replies
701
views
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
0
votes
3
replies
173
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 14 hours ago by 65k • written 1 day ago by • 0
1
vote
3
replies
558
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
votes
3
replies
418
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
3
replies
390
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 12 weeks 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
3
votes
3
replies
565
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
2
votes
3
replies
358
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
0
votes
3
replies
638
views
limma paired design
DifferentialExpression limma
updated 10 months ago by 65k • written 10 months ago by • 0
4
votes
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
2
replies
402
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
2
replies
223
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
5 weeks ago • updated 4 weeks ago Chanderkant Chaudhary • 0
0
votes
2
replies
337
views
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
2
replies
674
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
0
votes
2
replies
152
views
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
votes
2
replies
309
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 6 weeks ago by 41k • written 7 weeks ago by • 0
1
vote
2
replies
526
views
Contrast of Contrasts in Limma
limma DifferentialExpression
11 months ago mpitz • 0
0
votes
2
replies
743
views
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
votes
2
replies
286
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 weeks ago Shaimaa Gamal • 0
0
votes
2
replies
511
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
0
votes
2
replies
289
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 41k • written 3 months ago by • 0
0
votes
2
replies
206
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 21 days ago by 41k • written 25 days ago by ▴ 30
0
votes
2
replies
261
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by • 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
votes
1
reply
501
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
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
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
50 results • Page 1 of 1
Recent ...
Replies
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
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 …
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
Awards • All
Popular Question to junhui.li11 • 0
Scholar to James W. MacDonald 65k
Popular Question to jeffrey.maurer • 0
Centurion to Chris • 0
Commentator to Leonard Goldstein ▴ 200
Locations • All
The city by the bay, 36 minutes ago
Canada, 41 minutes ago
USA, 51 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Canada, 1 hour ago
Traffic: 400 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6