Showing : DESEq2 • reset
0
votes
0
replies
16
views
Differing results with DESeq2
DESeq2
2 hours ago • updated 1 hour ago hampsdiv • 0
0
votes
1
reply
67
views
DESeq2 - human data, weird results, troubleshooting
DESeq2
4 hours ago bd2000 ▴ 30
1
vote
2
replies
150
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
updated 5 hours ago by 68k • written 6 hours ago by • 0
0
votes
1
reply
500
views
DESeq2
org.Mmu.eg.db DESeq2 TimeCourse DMSOvsdrug RNASeqData
updated 6 days ago by ★ 4.8k • written 6 days ago by • 0
4
votes
6
replies
1.1k
views
Surprising behavior for DEXseq dispersion estimate plot?
DESeq2 DEXSeq
updated 7 days ago by ★ 4.8k • written 29 days ago by • 0
0
votes
0
replies
165
views
How do I set up my DESeq analysis when I know a few vehicle control samples provide background effects we don't want to see in any of the subsequent …
DESeq2 RUVSeq
10 days ago Simran • 0
1
vote
4
replies
370
views
DESEQ2 looking at main effects while controlling for a continuous variable
DESeq2
15 days ago • updated 10 days ago Lennie • 0
0
votes
4
replies
471
views
Guidance Needed: Best Practices for Handling Technical Replicates in RNA-seq Analysis
DESeq2 TechnicalReplicates RNASeq
written 17 days ago by • 0
1
vote
1
reply
773
views
Use of org.Rn.eg.db with GRCr8 reference genome
DESeq2 org.Rn.eg.db
updated 20 days ago by 68k • written 21 days ago by • 0
1
vote
2
replies
1.2k
views
[ChIP-seq] DESeq2 on counts matrix from union set of called peaks
csaw ChIPseq DESeq2 DiffBind
23 days ago • updated 22 days ago Luca • 0
0
votes
2
replies
421
views
Removing UTR from GTF for gene quantification
edgeR DESeq2
updated 18 days ago by 43k • written 26 days ago by ▴ 20
0
votes
1
reply
200
views
DESeq use in lipidomic analysis
DESeq2 package Lipidomics
updated 28 days ago by 43k • written 29 days ago by • 0
0
votes
3
replies
634
views
how many significant figures are there in DESeq2 output
DESeq2
updated 4 weeks ago by ★ 4.8k • written 4 weeks ago by ▴ 180
2
votes
5
replies
1.0k
views
Group-specific condition effects with individuals nested: matrix is not full rank
DESeq2
5 weeks ago picasa1983 • 0
3
votes
7
replies
2.0k
views
Vertical line at A=0, nothing else, on MA plot
deseq2
updated 5 weeks ago by ▴ 10 • written 6.1 years ago by ▴ 20
0
votes
1
reply
359
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 5 weeks ago by 68k • written 5 weeks ago by • 0
1
vote
1
reply
475
views
Interpreting DESEQ2 interaction term and inclusion of covariate
DESeq2
updated 5 weeks ago by ★ 1.4k • written 5 weeks ago by ▴ 10
1
vote
1
reply
304
views
DEseq2 design for additive treatment
DESeq2
updated 5 weeks ago by ★ 4.8k • written 5 weeks ago by • 0
2
votes
2
replies
555
views
Plot title for PCA in DESeq2
DESeq2
5 weeks ago AL • 0
0
votes
3
replies
577
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 weeks ago by 43k • written 6 weeks ago by • 0
1
vote
2
replies
1.1k
views
Weird p-values using DESeq2?
DESeq2 RNASeq
updated 6 weeks ago by ★ 4.8k • written 7 weeks ago by • 0
0
votes
1
reply
166
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 7 weeks ago by 43k • written 8 weeks ago by • 0
0
votes
3
replies
538
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 7 weeks ago by • 0 • written 8 weeks ago by • 0
0
votes
2
replies
393
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 7 weeks ago by • 0 • written 8 weeks ago by • 0
0
votes
3
replies
456
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
updated 5 weeks ago by • 0 • written 8 weeks ago by • 0
0
votes
3
replies
440
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat RNASeq DESeq2 scRNAseq
updated 8 weeks ago by • 0 • written 9 weeks ago by ▴ 10
0
votes
1
reply
244
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 weeks ago by 43k • written 9 weeks ago by • 0
2
votes
2
replies
477
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 9 weeks ago by ★ 1.4k • written 10 weeks ago by • 0
0
votes
4
replies
998
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq DESeq2
9 weeks ago Quang NN ▴ 10
0
votes
2
replies
629
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot DESeq2
10 weeks ago Blandine • 0
0
votes
5
replies
385
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 weeks ago by • 0
0
votes
4
replies
575
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
10 weeks ago Quang NN ▴ 10
2
votes
5
replies
465
views
Differential variability modelling with vst() expression
limma DESeq2
written 12 weeks ago by • 0
0
votes
3
replies
600
views
DESeq2 analysis with transcript counts
Transcriptomics RNASeq DESeq2
written 12 weeks ago by • 0
2
votes
9
replies
1.1k
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2 BatchEffect
12 weeks ago • updated 10 weeks ago Quang NN ▴ 10
1
vote
1
reply
480
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond DESeq2 rnaseqDTU
updated 12 weeks ago by 43k • written 12 weeks ago by • 0
0
votes
1
reply
226
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by • 0
0
votes
1
reply
423
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
2
votes
1
reply
428
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2 RNASeqData
updated 3 months ago by 43k • written 3 months ago by • 0
0
votes
2
replies
431
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
3 months ago Kucsera • 0
1
vote
1
reply
443
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 3 months ago by 43k • written 3 months ago by • 0
1
vote
9
replies
1.0k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
4
votes
2
replies
571
views
Standardization of rlog transformed counts before PCA
RNASeq DESeq2 Visualization
updated 3 months ago by ★ 4.8k • written 3 months ago by ▴ 10
1
vote
5
replies
695
views
Deseq2 Design
RNASeq DESeq2
updated 3 months ago by 68k • written 3 months ago by • 0
0
votes
5
replies
719
views
p value is 0, padj is 0
DESeq2
3 months ago Wirayatida • 0
1
vote
2
replies
691
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport DESeq2 GSVA
3 months ago georgii.vdovin • 0
0
votes
7
replies
1.0k
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 3 months ago by • 0 • written 3 months ago by • 0
0
votes
1
reply
390
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 3 months ago by 43k • written 3 months ago by ▴ 20
0
votes
3
replies
535
views
DESeq2 - Comparing Comparisons
DESeq2
updated 3 months ago by 68k • written 4 months ago by • 0
0
votes
4
replies
666
views
lfcShrink and alpha value
lfcShrink DESeq2
4 months ago cropero • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
Awards • All
Popular Question to bd2000 ▴ 30
Popular Question to shepherl 4.1k
Scholar to Michael Love 43k
Popular Question to Rob • 0
Popular Question to Gordon Smyth 52k
Locations • All
Seattle, WA, United States, 5 minutes ago
United States, 21 minutes ago
United States, 22 minutes ago
United States, 24 minutes ago
United Kingdom, 28 minutes ago
Traffic: 721 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