Showing : differentialexpression • reset
5
votes
6
replies
341
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 3 days ago by ★ 4.0k • written 7 days ago by ▴ 30
1
vote
3
replies
208
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 10 days ago by 65k • written 11 days ago by • 0
0
votes
2
replies
125
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 11 days ago by 65k • written 11 days ago by • 0
0
votes
2
replies
165
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 6 days ago by 41k • written 11 days ago by ▴ 30
1
vote
2
replies
195
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
25 days ago • updated 20 days ago Chanderkant Chaudhary • 0
5
votes
3
replies
658
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 19 days ago by 50k • written 26 days ago by ▴ 50
0
votes
2
replies
240
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
2
replies
288
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 4 weeks ago by 41k • written 4 weeks ago by • 0
3
votes
4
replies
354
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
0
votes
4
replies
259
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
6 weeks ago mperalc • 0
0
votes
0
replies
185
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
8 weeks ago Abril • 0
2
votes
1
reply
270
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 8 weeks ago by ★ 4.0k • written 8 weeks ago by • 0
3
votes
2
replies
255
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
9 weeks ago Shaimaa Gamal • 0
4
votes
3
replies
309
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
2
votes
3
replies
325
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
3
replies
348
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 10 weeks ago by • 0
2
votes
1
reply
198
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 10 weeks ago by 41k • written 10 weeks ago by ▴ 20
0
votes
2
replies
265
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 10 weeks ago by 41k • written 10 weeks ago by • 0
5
votes
6
replies
511
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 weeks ago Shaimaa Gamal • 0
4
votes
6
replies
531
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 9 weeks ago by 50k • written 3 months ago by • 0
3
votes
1
reply
245
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
5
replies
580
views
Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 11 weeks ago Lucy ▴ 60
0
votes
3
replies
400
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
1
vote
1
reply
372
views
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
1
vote
3
replies
552
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 3 months ago by • 0
2
votes
4
replies
472
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
0
votes
2
replies
313
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
4 months ago Luca • 0
1
vote
2
replies
365
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
1
reply
316
views
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
1
vote
4
replies
518
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
8
replies
784
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
5 months ago Luca • 0
0
votes
0
replies
335
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
6 months ago nromerov • 0
2
votes
6
replies
741
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
2
votes
4
replies
639
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
6 months ago Shihui • 0
0
votes
1
reply
392
views
''Model_Matrix'' error
DifferentialExpression limma
updated 6 months ago by 50k • written 6 months ago by • 0
3
votes
3
replies
555
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 6 months ago by 65k • written 6 months ago by • 0
0
votes
3
replies
437
views
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
0
votes
2
replies
478
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
7 months ago Beyza • 0
0
votes
1
reply
485
views
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
votes
1
reply
361
views
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
1
vote
3
replies
529
views
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
0
votes
0
replies
424
views
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
0
votes
6
replies
741
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
2
replies
656
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
9 months ago Matteo • 0
1
vote
1
reply
510
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
0
votes
3
replies
624
views
limma paired design
DifferentialExpression limma
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
1
reply
485
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
8
replies
1.4k
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
1
vote
0
replies
448
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 10 months ago by 41k • written 10 months ago by ▴ 20
2
votes
6
replies
932
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 9 months ago by 3.8k • written 10 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: flowStats Search Error by James W. MacDonald 65k
A better approach is to click on the Packages header on the main site, then search on that page for flowStats, rather than searching the en…
Comment: geneList error in clusterprofiler by Ana • 0
Ahh thank you, that fixed it!
Answer: geneList error in clusterprofiler by Basti ▴ 750
Have a look at the documentation : https://www.rdocumentation.org/packages/clusterProfiler/versions/3.0.4/topics/gseGO geneList argument s…
Comment: Memory errors using read.bismark? by Juan Higareda • 0
Thanks again for your answer, I will try to play a little bit with the parameters. Only one thing, my data are actually CpG methylation :)…
Comment: flowStats Search Error by tholmes • 0
Thank you so much!
Votes
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
Comment: [DiffBind] Obtaining normalization factors
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Awards • All
Popular Question to paria.alipour • 0
Popular Question to Eman • 0
Popular Question to James W. MacDonald 65k
Scholar to nhaus ▴ 30
Popular Question to shepherl 3.8k
Locations • All
Ghana/KNUST, just now
United States, 3 minutes ago
France, 4 minutes ago
United States, 12 minutes ago
Brazil, 24 minutes ago
Traffic: 842 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