Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
DESeq2
•
reset
0
votes
1
reply
45
views
Plot title for PCA in DESeq2
DESeq2
updated 6 hours ago by
ATpoint
★ 4.7k • written 12 hours ago by
AL
• 0
0
votes
3
replies
384
views
Differential variance analysis - can i use deseq2
DESeq2
DifferentialExpression
RNASeq
RNASeqData
scRNAseq
updated 1 day ago by
Michael Love
43k • written 3 days ago by
Marwan
• 0
1
vote
2
replies
977
views
Weird p-values using DESeq2?
DESeq2
RNASeq
updated 7 days ago by
ATpoint
★ 4.7k • written 8 days ago by
ingrid.h
• 0
0
votes
1
reply
128
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 11 days ago by
Michael Love
43k • written 15 days ago by
Sahil
• 0
0
votes
3
replies
450
views
DESeq2 adujsted p-value cutoff seemingly not working
DESeq2
updated 11 days ago by
980linnet
• 0 • written 16 days ago by
Guilherme
• 0
0
votes
2
replies
337
views
accounting for vs. removing batch effects with DESeq2 in RNAseq analysis
DESeq2
updated 14 days ago by
Blair
• 0 • written 19 days ago by
A
• 0
0
votes
2
replies
307
views
displaying the differential expression with deseq2 over 4X2 samples with the individual changes in gene expression per sample
DESeq2
19 days ago • updated 18 days ago
Martijn
• 0
0
votes
3
replies
355
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 19 days ago by
jodan
• 0 • written 27 days ago by
Quang NN
▴ 10
0
votes
1
reply
157
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression
RNASeq
DESeq2
updated 24 days ago by
Michael Love
43k • written 25 days ago by
Sim
• 0
2
votes
2
replies
432
views
Selection of correct coefficients or contrasts in DESeq2
DESeq2
updated 25 days ago by
swbarnes2
★ 1.4k • written 29 days ago by
Nathan
• 0
0
votes
4
replies
930
views
Why select top highly expressed genes based on normalized counts, but then plot VST-transformed values in DESeq2 pheatmap?
RNASeq
DESeq2
27 days ago • updated 25 days ago
Quang NN
▴ 10
0
votes
2
replies
374
views
How to generate circular cnetplot and color nodes and edges in the same plot ?
cnetplot
DESeq2
4 weeks ago • updated 29 days ago
Blandine
• 0
0
votes
5
replies
322
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2
DifferentialExpression
RNASeqData
BatchEffect
written 4 weeks ago by
georgeyu703
• 0
0
votes
4
replies
466
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2
GSEA
clusterProfiler
4 weeks ago
Quang NN
▴ 10
2
votes
5
replies
375
views
Differential variability modelling with vst() expression
limma
DESeq2
written 6 weeks ago by
jtsy6383
• 0
0
votes
3
replies
523
views
DESeq2 analysis with transcript counts
Transcriptomics
RNASeq
DESeq2
written 6 weeks ago by
sindhuri
• 0
2
votes
9
replies
915
views
Why did PCA plots look exactly the same after adjusting for batch covariate in DESeq2 design?
DESeq2
BatchEffect
6 weeks ago • updated 4 weeks ago
Quang NN
▴ 10
1
vote
1
reply
362
views
Considerations behind the choice of RNAseq Differential Expression Analysis Tools
fishpond
DESeq2
rnaseqDTU
updated 6 weeks ago by
Michael Love
43k • written 6 weeks ago by
muhammadsohailraza
• 0
0
votes
1
reply
200
views
Want numbers in DESeq to be seen as numerical, not categorical
DESeq2
updated 6 weeks ago by
swbarnes2
★ 1.4k • written 6 weeks ago by
natalievillafranca
• 0
0
votes
1
reply
382
views
Please, I desperately need help with DESeq2. Three groups of repeated measures with two timepoints... (plus an additional group)
edgeR
DESeq2
updated 7 weeks ago by
Michael Love
43k • written 8 weeks ago by
Jimmy Mak
• 0
2
votes
1
reply
380
views
Is it possible to work with DESeq2 where data is not properly matched for sex and age
DESeq2
RNASeqData
updated 7 weeks ago by
Michael Love
43k • written 8 weeks ago by
KR
• 0
0
votes
2
replies
341
views
DESeq error: counts matrix should be numeric, currently it has mode: character
DESeq2
7 weeks ago
Kucsera
• 0
1
vote
1
reply
397
views
Can DESeq2's design compensate for sequencing experimental design shortcomings?
DESeq2
updated 9 weeks ago by
Michael Love
43k • written 10 weeks ago by
txema.heredia
• 0
1
vote
9
replies
893
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma
DESeq2
edgeR
written 9 weeks ago by
anna.cot.anna.cot
▴ 30
4
votes
2
replies
445
views
Standardization of rlog transformed counts before PCA
RNASeq
DESeq2
Visualization
updated 9 weeks ago by
ATpoint
★ 4.7k • written 10 weeks ago by
bbao
▴ 10
1
vote
5
replies
619
views
Deseq2 Design
RNASeq
DESeq2
updated 9 weeks ago by
James W. MacDonald
68k • written 10 weeks ago by
pm_25
• 0
0
votes
5
replies
582
views
p value is 0, padj is 0
DESeq2
10 weeks ago
Wirayatida
• 0
1
vote
2
replies
565
views
Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
10 weeks ago
georgii.vdovin
• 0
0
votes
7
replies
896
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 10 weeks ago by
txema.heredia
• 0 • written 10 weeks ago by
fjrsa
• 0
0
votes
1
reply
324
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 11 weeks ago by
Michael Love
43k • written 11 weeks ago by
bhandary.8590
▴ 20
0
votes
3
replies
462
views
DESeq2 - Comparing Comparisons
DESeq2
updated 10 weeks ago by
James W. MacDonald
68k • written 11 weeks ago by
sk
• 0
0
votes
4
replies
597
views
lfcShrink and alpha value
lfcShrink
DESeq2
12 weeks ago • updated 11 weeks ago
cropero
• 0
2
votes
1
reply
347
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 11 weeks ago by
Michael Love
43k • written 12 weeks ago by
Nikita
• 0
0
votes
2
replies
255
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 11 weeks ago by
Michael Love
43k • written 11 weeks ago by
Sam
• 0
0
votes
2
replies
297
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
12 weeks ago
Anna
• 0
1
vote
2
replies
596
views
Deseq2 res Function
DESeq2
updated 12 weeks ago by
James W. MacDonald
68k • written 3 months ago by
sap275
▴ 10
0
votes
4
replies
484
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
3 months ago
NB
• 0
0
votes
5
replies
512
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 3 months ago by
Michael Love
43k • written 3 months ago by
maripane
• 0
0
votes
1
reply
288
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 3 months ago by
James W. MacDonald
68k • written 3 months ago by
rj1435
• 0
1
vote
2
replies
349
views
Differene between the Wald and LRT test for time-series gene expression data
DESeq2
3 months ago
Denise
• 0
0
votes
1
reply
199
views
eRNAs count
RNASeq
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
Irene
• 0
0
votes
1
reply
445
views
DESeq2 rerun returns different results
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
wl1111
• 0
0
votes
1
reply
306
views
Is my time course analysis with DESeq2 valid?
GeneExpression
DESeq2
TimeCourse
updated 3 months ago by
Michael Love
43k • written 3 months ago by
Jason
• 0
0
votes
1
reply
284
views
DESeq2 "Not full rank" and "less than full rank" error
DESeq2
deseq
updated 3 months ago by
Guido Hooiveld
★ 4.1k • written 3 months ago by
Najla Abassi
• 0
2
votes
2
replies
704
views
Handling biological replicates in DESeq2
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
sk
• 0
5
votes
2
replies
26k
views
DESeq2: thousands of NA for pvalues?
deseq2
rna-seq
DEGs
cooks cutoff
updated 27 days ago by
fuqichen1
• 0 • written 6.1 years ago by
aishu.jp
▴ 30
1
vote
6
replies
1.1k
views
Volcano plot has many values around zero
RNA-seq
DESeq2
volcanoplot
updated 3 months ago by
Michael Love
43k • written 3 months ago by
nramakr
▴ 10
0
votes
2
replies
434
views
DESeq2 interaction between cancer cells and microenvironment cells
DESeq2
written 3 months ago by
ballackselma
• 0
4
votes
5
replies
766
views
DESeq Input from Salmon + tximport/tximeta
tximportData
summarizeToGene
tximport
DESeq2
salmon
3 months ago
LuciaNhu
• 0
0
votes
1
reply
466
views
Average expression of genes across replicates
DESeq2
updated 3 months ago by
ATpoint
★ 4.7k • written 3 months ago by
James
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: WGCNA with paired samples
by
Ivo
• 0
You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …
Answer: Plot title for PCA in DESeq2
by
ATpoint
★ 4.7k
The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
Comment: DESeq2 It is correct to use interaction term for patient variability?
by
Bradley
• 0
I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
Comment: Differential variance analysis - can i use deseq2
by
Michael Love
43k
VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
Answer: Use of limma R package with targeted proteomics for DE analysis
by
Gordon Smyth
52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
Awards
• All
Popular Question
to
leakerb
• 0
Popular Question
to
Mark Dunning
★ 1.1k
Popular Question
to
shepherl
4.1k
Popular Question
to
Hugo Varet
▴ 80
Popular Question
to
Fred Hutch (Recruiting)
▴ 40
Locations
• All
United States,
14 minutes ago
Sheffield, Uk,
1 hour ago
Seattle, WA, United States,
1 hour ago
Switzerland,
2 hours ago
Türkiye,
2 hours ago
Traffic: 627 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