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DESeq2
•
reset
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 18 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
6
votes
19
replies
2.5k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 6 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
3
votes
3
replies
228
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 13 days ago by
Michael Love
41k • written 14 days ago by
WardDeb
• 0
3
votes
3
replies
237
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 7 days ago by
ATpoint
★ 4.1k • written 8 days ago by
bioinf
▴ 10
3
votes
1
reply
315
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 13 days ago by
Michael Love
41k • written 13 days ago by
i.sudbery
▴ 40
2
votes
5
replies
753
views
DESeq2 setting significant p-value
DESeq2
updated 17 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 19 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
3
replies
176
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 1 day ago by
ATpoint
★ 4.1k • written 3 days ago by
Reza
• 0
2
votes
9
replies
392
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 11 days ago by
James W. MacDonald
65k • written 11 days ago by
Alexandre
• 0
1
vote
4
replies
481
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 5 days ago
JKim
• 0
1
vote
1
reply
110
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 6 days ago by
Michael Love
41k • written 6 days ago by
marcusn
• 0
1
vote
4
replies
332
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
12 days ago • updated 10 days ago
winwater0928
• 0
1
vote
3
replies
216
views
Different Shrunk Log2FC according with reference
DESeq2
updated 12 days ago by
Michael Love
41k • written 12 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
26 days ago • updated 17 days ago
Weiqian
▴ 10
1
vote
3
replies
222
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 10 days ago by
Michael Love
41k • written 11 days ago by
JalapenoCornbread
• 0
1
vote
2
replies
197
views
Design Matrix within group comparison more than two groups
DESeq2
24 days ago • updated 23 days ago
hemantcnaik
• 0
1
vote
1
reply
100
views
Handling multiple differential expression comparisons
DESeq2
updated 1 day ago by
Michael Love
41k • written 3 days ago by
Zainab
▴ 10
1
vote
2
replies
714
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
19 days ago • updated 10 days ago
ussarizona
▴ 10
0
votes
3
replies
207
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 20 days ago by
Michael Love
41k • written 21 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
165
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 27 days ago by
Michael Love
41k • written 27 days ago by
Adelaide
• 0
0
votes
1
reply
103
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Agung
• 0
0
votes
2
replies
123
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
6 days ago • updated 3 days ago
Aurora
• 0
0
votes
1
reply
110
views
putting my own expression data in deseq2
DESeq2
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
Dev
• 0
0
votes
2
replies
223
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 27 days ago by
Michael Love
41k • written 4 weeks ago by
nhaus
▴ 30
0
votes
3
replies
252
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
HAK
• 0
0
votes
1
reply
144
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
angelathuynh5
• 0
0
votes
2
replies
138
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
5 days ago • updated 4 days ago
kcarey
• 0
0
votes
3
replies
136
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 4 days ago by
ATpoint
★ 4.1k • written 5 days ago by
james.zhang20
• 0
0
votes
1
reply
132
views
Deseq2 Rlog transformation
DESeq2
updated 21 days ago by
ATpoint
★ 4.1k • written 22 days ago by
Sahar
• 0
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 17 days ago by
Michael Love
41k • written 22 days ago by
Rajat
• 0
0
votes
2
replies
107
views
DESeq2 v1.35.0
DESeq2
updated 4 days ago by
Michael Love
41k • written 4 days ago by
Espresso
• 0
0
votes
7
replies
423
views
DESeq filtering specific to contrasts
DESeq2
updated 17 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
0
votes
6
replies
214
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 2 days ago by
swbarnes2
★ 1.3k • written 4 days ago by
arfranco
▴ 130
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 18 days ago by
Michael Love
41k • written 20 days ago by
Brynn
• 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
26 days ago • updated 25 days ago
Shefali
• 0
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 19 days ago by
quanah.hudson
• 0
0
votes
4
replies
238
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
19 days ago • updated 16 days ago
lonn
• 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 18 days ago by
Michael Love
41k • written 18 days ago by
09191919
• 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 18 days ago by
Michael Love
41k • written 18 days ago by
ishij9717
• 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 27 days ago by
Michael Love
41k • written 4 weeks ago by
kys91240
• 0
0
votes
4
replies
602
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 20 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
0
votes
8
replies
351
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 11 days ago by
swbarnes2
★ 1.3k • written 13 days ago by
Aaliya
• 0
0
votes
1
reply
155
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 12 days ago by
Michael Love
41k • written 12 days ago by
kcarey
• 0
0
votes
2
replies
210
views
PCA plot suggestions
DESeq2
PCAtools
updated 10 days ago by
Michael Love
41k • written 12 days ago by
Aaliya
• 0
0
votes
1
reply
134
views
Bioinformatics student
Des
DESeq2
updated 24 days ago by
hemantcnaik
• 0 • written 24 days ago by
Sahar
• 0
45 results • Page
1 of 1
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Awards
• All
Scholar
to
Michael Love
41k
Popular Question
to
Malcolm Cook
★ 1.6k
Teacher
to
Gordon Smyth
50k
Popular Question
to
priyanka.m
• 0
Popular Question
to
Vincent J. Carey, Jr.
6.7k
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