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DESeq2
•
reset
0
votes
0
replies
14
views
Plot PCA with ellipses using ggplot
DESeq2
ggplot
PCA
1 hour ago
robledoj13
• 0
4
votes
12
replies
524
views
DGE with a Continuous Variable
DESeq2
model
updated 11 hours ago by
Michael Love
42k • written 10 days ago by
picasa1983
• 0
3
votes
5
replies
249
views
A question occur when using DESeq2 on a complex design
DESeq2
rnaseqGene
RNASeq
1 day ago
MedocRafael
• 0
1
vote
8
replies
3.1k
views
Significantly regulated genes produced by only a few affected samples
deseq2
written 6.4 years ago by
serpalma.v
▴ 60
4
votes
2
replies
707
views
DESeq fitNbinomGLMs Warning Issue: In fitNbinomGLMs(objectNZ[fitidx, , drop = FALSE], alpha_hat = alpha_hat[fitidx], : 4189rows had non-positive e…
DESeq2
RNAseq
8 days ago • updated 1 day ago
mila
▴ 10
0
votes
0
replies
141
views
DESeq2 Likelihood ratio test + contrast option + Volcano plot
DESeq2
volcanoplot
LRT
2 days ago
Eric
• 0
0
votes
3
replies
269
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData
DESeq2
RNASeq
DifferentialExpression
updated 3 days ago by
ATpoint
★ 4.2k • written 3 days ago by
Mark
• 0
1
vote
3
replies
299
views
Doubt about model in paired samples (intercept ?)
DESeq2
updated 4 days ago by
Michael Love
42k • written 6 days ago by
picasa1983
• 0
0
votes
2
replies
728
views
How to correct for a covariate in DESeq2 that is linear with the condition of interest
DESeq2
7 days ago • updated 4 days ago
Fiona
• 0
0
votes
10
replies
621
views
Two treatments, one control
DESeq2
stageR
16 days ago • updated 4 days ago
alephreish
• 0
2
votes
3
replies
260
views
DeSeq2 Model Problems with species, tissue, and tissue status nesting
DESeq2
R
written 8 days ago by
tbiewerh
• 0
3
votes
8
replies
24k
views
Deseq: What does "BaseMean" mean?
deseq2
written 5.9 years ago by
183227851
• 0
0
votes
1
reply
117
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 8 days ago by
ATpoint
★ 4.2k • written 8 days ago by
picasa1983
• 0
0
votes
0
replies
116
views
DESeq2 - Outliers influencing sig DEGs, filter counts per group samples, not by all samples
filtering
DESeq2
outliers
9 days ago
smac_head
• 0
1
vote
5
replies
385
views
DESeq2 ML Query
DESeq2
updated 10 days ago by
Michael Love
42k • written 5 weeks ago by
chris2.a.white
• 0
2
votes
3
replies
376
views
DESeq normalized counts vs CQN and statistics
DESeq2
cqn
updated 11 days ago by
Michael Love
42k • written 15 days ago by
emlucero
• 0
1
vote
2
replies
321
views
DESeq2: two conditions two genotypes
DESeq2
15 days ago • updated 12 days ago
Rocio
• 0
0
votes
1
reply
212
views
Problem with spike-ins (ERCC) in DESeq2 analysis after doing RUVg!
SpikeIn
RUVSeq
DESeq2
RUV
updated 15 days ago by
Michael Love
42k • written 19 days ago by
Ειρήνη
• 0
1
vote
8
replies
480
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2
glmGamPoi
offset
edgeR
scRNAseq
updated 18 days ago by
Gordon Smyth
51k • written 4 weeks ago by
Alec
• 0
0
votes
1
reply
148
views
unreal negative log2fc values
DESeq2
des
updated 21 days ago by
James W. MacDonald
66k • written 21 days ago by
Atul K.
• 0
0
votes
0
replies
151
views
What does evidence of batch effect in bulk rnaseq look like?
surrogatevariables
DESeq2
BatchEffect
bulkrna-seq
sva-seq
23 days ago • updated 22 days ago
BioinfGuru
▴ 30
0
votes
1
reply
223
views
LRT test for different timepoints (one tissue types vs. many tissue types)
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
K
• 0
2
votes
1
reply
663
views
DESeq2 time course using fitted splines
RNASeqData
TimeCourse
DESeq2
timecoursedata
updated 28 days ago by
Michael Love
42k • written 12 months ago by
georgii.vdovin
• 0
2
votes
3
replies
4.1k
views
Deseq2 use fpkm
deseq2
updated 29 days ago by
Michael Love
42k • written 7.8 years ago by
jarod_v6@libero.it
▴ 40
1
vote
2
replies
1.1k
views
Why does DESeq2 give negative log2 fold change in treatment vs control for some genes when normalized counts are higher in treatment.
DESeq2
4 weeks ago
sropri
• 0
17
votes
11
replies
34k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 4 weeks ago by
Michael Love
42k • written 8.5 years ago by
ribioinfo
▴ 100
0
votes
1
reply
172
views
Deseq2 design matrix
DESeq2
Designmatrix
limma
updated 4 weeks ago by
James W. MacDonald
66k • written 4 weeks ago by
Neha
• 0
2
votes
5
replies
520
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 4 weeks ago by
ATpoint
★ 4.2k • written 12 weeks ago by
Reza
• 0
1
vote
1
reply
187
views
DESeq2 - vst() - log2FC - no replicates
DESeq2
log2FC
vst()
updated 5 weeks ago by
ATpoint
★ 4.2k • written 5 weeks ago by
lifeonmars
• 0
0
votes
2
replies
256
views
Test of Multiple Linear Combination on coefficients from Wald Test in Deseq2
Regression
DESeq2
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
David W. H.
• 0
0
votes
1
reply
211
views
Significant genes in DESeq2 analysis
DESeq2
RNASeq
updated 5 weeks ago by
James W. MacDonald
66k • written 5 weeks ago by
cbio
• 0
0
votes
3
replies
331
views
Combining two bulk RNA seq datasets
RNASeqData
DESeq2
Normalization
5 weeks ago
Tanvi
• 0
1
vote
9
replies
606
views
Most enriched pathway is not expressed when modifying universe parameter
DESeq2
clusterProfiler
Pathways
RNASeq
org.Mm.eg.db
updated 5 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
adrip
• 0
0
votes
1
reply
959
views
In a 3 group DEG analysis with three batches, can I use 1 group in all three batches to correct for the batch effect?
DESeq2
updated 6 weeks ago by
Michael Love
42k • written 7 weeks ago by
prabath_meemaduma
• 0
2
votes
1
reply
323
views
Design formula, numeric contrast, and lfcshrink in deseq2
DESeq2
updated 6 weeks ago by
Michael Love
42k • written 6 weeks ago by
hx
▴ 10
2
votes
1
reply
233
views
DESeq2 returns results for group with just one replicate
DESeq2
DifferentialExpression
updated 6 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
nhaus
▴ 50
2
votes
1
reply
352
views
Handling multiple differential expression comparisons
DESeq2
12 weeks ago • updated 6 weeks ago
Zainab
▴ 10
1
vote
3
replies
332
views
Including infectivity information to RNA-Seq analysis
RNASeqData
DESeq2
RNA-Seq
RNASeq
updated 6 weeks ago by
James W. MacDonald
66k • written 6 weeks ago by
Ben
▴ 50
3
votes
6
replies
1.9k
views
Multiple factor DSEq2 result generates weird volcano plot
DESeq2
updated 6 weeks ago by
ATpoint
★ 4.2k • written 15 months ago by
liuyang32201220
▴ 20
2
votes
2
replies
220
views
Double normalising when using sva and deseq2
DESeq2
Normalisation
Bulkrnaseq
Svaseq
6 weeks ago
BioinfGuru
▴ 30
4
votes
5
replies
1.4k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 6 weeks ago by
ij283
• 0 • written 15 months ago by
Bernardo
▴ 10
0
votes
1
reply
192
views
Can we compare 3 different experimental conditions with DESeq2?
DESeq2
StatisticalMethod
updated 7 weeks ago by
swbarnes2
★ 1.4k • written 7 weeks ago by
Esteban
• 0
1
vote
2
replies
420
views
Cohen's D calculation for differentially expressed genes via DESeq2 results summary stats
DESeq2
7 weeks ago
a_p
• 0
3
votes
5
replies
2.7k
views
Plot PC1 and PC4 in plotPCA function
DESeq2
plotPCA
updated 7 weeks ago by
Daniele
• 0 • written 2.5 years ago by
synat.keam
• 0
0
votes
1
reply
198
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData
DESeq2
DifferentialExpression
updated 7 weeks ago by
James W. MacDonald
66k • written 7 weeks ago by
ZhuYi
• 0
1
vote
2
replies
2.0k
views
using tximport with STAR transcript-quantification output
tximport
deseq2
STAR
updated 7 weeks ago by
rodrigo.duarte88
▴ 40 • written 4.7 years ago by
mohamedrefaat.1.1992
• 0
1
vote
4
replies
1.1k
views
Problem in running DESeq from expected count data of Transcriptome by Trinity followed by RSEM
Tissue
Spati
RSEM
deno
DEseq2
written 14 months ago by
shashank
• 0
0
votes
1
reply
218
views
multiple condition issue running DESeq
DESeq2
updated 7 weeks ago by
Michael Love
42k • written 7 weeks ago by
Kelly
• 0
0
votes
3
replies
326
views
Ploting of normalized counts after batch removal
DESeq2
updated 7 weeks ago by
Gordon Smyth
51k • written 7 weeks ago by
altuda
▴ 10
0
votes
9
replies
958
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 7 weeks ago by
BioinfGuru
▴ 30 • written 10 weeks ago by
Eric Katagirya
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
▴ 730
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▴ 180
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to
Michael Love
42k
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Leonardo Collado Torres
★ 1.1k
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Gordon Smyth
51k
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