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
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 29 days ago by
Elizabeth
• 0 • written 8.9 years ago by
gthm
▴ 30
6
votes
19
replies
2.6k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 17 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
4
votes
9
replies
230
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 1 day ago by
ATpoint
★ 4.1k • written 2 days ago by
pangtaihin
• 0
3
votes
3
replies
268
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
bioinf
▴ 10
3
votes
3
replies
250
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 24 days ago by
Michael Love
42k • written 25 days ago by
WardDeb
• 0
3
votes
1
reply
328
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 24 days ago by
Michael Love
42k • written 24 days ago by
i.sudbery
▴ 40
2
votes
7
replies
363
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
9 days ago • updated 6 days ago
sajadahmad41454
• 0
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 12 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Reza
• 0
2
votes
5
replies
791
views
DESeq2 setting significant p-value
DESeq2
updated 28 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
2
votes
9
replies
426
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 22 days ago by
James W. MacDonald
65k • written 22 days ago by
Alexandre
• 0
1
vote
3
replies
253
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 21 days ago by
Michael Love
42k • written 22 days ago by
JalapenoCornbread
• 0
1
vote
2
replies
738
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago
Patadù
▴ 10
1
vote
3
replies
303
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 9 days ago by
ATpoint
★ 4.1k • written 16 days ago by
angelathuynh5
• 0
1
vote
1
reply
185
views
Handling multiple differential expression comparisons
DESeq2
updated 12 days ago by
Michael Love
42k • written 14 days ago by
Zainab
▴ 10
1
vote
1
reply
155
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 17 days ago by
Michael Love
42k • written 17 days ago by
marcusn
• 0
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 23 days ago by
Michael Love
42k • written 23 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
526
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 16 days ago
JKim
• 0
1
vote
2
replies
225
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
DESeq2
eigencorplot
PCAtools
4 days ago • updated 1 day ago
BioinfGuru
▴ 30
1
vote
2
replies
262
views
How to retrieve detailed regression results from deseq2
DESeq2
5 weeks ago • updated 28 days ago
Weiqian
▴ 10
1
vote
4
replies
356
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
23 days ago • updated 21 days ago
winwater0928
• 0
0
votes
1
reply
124
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 29 days ago by
Michael Love
42k • written 29 days ago by
09191919
• 0
0
votes
2
replies
226
views
PCA plot suggestions
DESeq2
PCAtools
updated 21 days ago by
Michael Love
42k • written 23 days ago by
Aaliya
• 0
0
votes
2
replies
159
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 0
0
votes
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 17 days ago by
Dev
• 0
0
votes
1
reply
44
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
13 hours ago • updated 12 hours ago
shaunpeterson
• 0
0
votes
1
reply
165
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 29 days ago by
ATpoint
★ 4.1k • written 4 weeks ago by
quanah.hudson
• 0
0
votes
1
reply
83
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
updated 3 days ago by
Michael Love
42k • written 4 days ago by
piemmea
• 0
0
votes
8
replies
383
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 23 days ago by
swbarnes2
★ 1.4k • written 24 days ago by
Aaliya
• 0
0
votes
2
replies
209
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
16 days ago • updated 15 days ago
kcarey
• 0
0
votes
1
reply
99
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
0
votes
2
replies
166
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
17 days ago • updated 14 days ago
Aurora
• 0
0
votes
1
reply
149
views
covariate with negative and positive values
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Brynn
• 0
0
votes
6
replies
290
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 14 days ago by
swbarnes2
★ 1.4k • written 15 days ago by
arfranco
▴ 130
0
votes
1
reply
165
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 23 days ago by
Michael Love
42k • written 23 days ago by
kcarey
• 0
0
votes
3
replies
219
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 15 days ago by
ATpoint
★ 4.1k • written 16 days ago by
james.zhang20
• 0
0
votes
2
replies
1.5k
views
How to use spike-in information (sequences from another species) with DESeq2::DESeq()
DESeq2
SpikeIn
Normalization
updated 7 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
0
votes
2
replies
99
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 1 hour ago by
JKim
• 0 • written 20 hours ago by
Ken C
• 0
0
votes
1
reply
138
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 17 days ago by
Michael Love
42k • written 18 days ago by
Agung
• 0
0
votes
4
replies
291
views
DEG with low counts
DESeq2
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
0
votes
8
replies
481
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
updated 3 days ago by
BioinfGuru
▴ 30 • written 4 days ago by
Eric Katagirya
• 0
0
votes
7
replies
445
views
DESeq filtering specific to contrasts
DESeq2
updated 28 days ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
0
votes
1
reply
155
views
rlog transformation
DESeq2
updated 29 days ago by
Michael Love
42k • written 29 days ago by
ishij9717
• 0
0
votes
3
replies
101
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 2 days ago by
Michael Love
42k • written 3 days ago by
Kasper
• 0
0
votes
1
reply
160
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
sajadahmad41454
• 0
0
votes
4
replies
263
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
4 weeks ago • updated 27 days ago
lonn
• 0
0
votes
3
replies
300
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 16 days ago by
Michael Love
42k • written 17 days ago by
HAK
• 0
46 results • Page
1 of 1
Recent ...
Replies
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Comment: STRINGdb : error with string_db$plot_network()
by
damian.szk
▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
Awards
• All
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
Koen Van den Berge
▴ 180
Popular Question
to
shepherl
3.9k
Popular Question
to
Ken C
• 0
Popular Question
to
Johannes Rainer
★ 2.0k
Locations
• All
France/Marseille/Inserm,
3 minutes ago
India,
30 minutes ago
United States,
53 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
Melbourne, Australia,
1 hour ago
Traffic: 382 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