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DeSeq2
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0
votes
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replies
5
views
Can I trust the differential expression analysis when the two groups overlap on the PCA?
DESeq2
pcaExplorer
46 minutes ago
Eric Katagirya
• 0
0
votes
0
replies
16
views
normalization across different species for DESeq2 analysis
DESeq2
normalization
Normalization
acrossspecies
3 hours ago
piemmea
• 0
0
votes
1
reply
86
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
sajadahmad41454
• 0
0
votes
1
reply
75
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
sajadahmad41454
• 0
2
votes
7
replies
296
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
5 days ago • updated 2 days ago
sajadahmad41454
• 0
2
votes
3
replies
223
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 8 days ago by
ATpoint
★ 4.1k • written 10 days ago by
Reza
• 0
1
vote
1
reply
160
views
Handling multiple differential expression comparisons
DESeq2
updated 8 days ago by
Michael Love
42k • written 10 days ago by
Zainab
▴ 10
0
votes
6
replies
258
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 9 days ago by
swbarnes2
★ 1.4k • written 10 days ago by
arfranco
▴ 130
0
votes
2
replies
141
views
DESeq2 v1.35.0
DESeq2
updated 11 days ago by
Michael Love
42k • written 11 days ago by
Espresso
• 0
0
votes
2
replies
189
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
11 days ago • updated 10 days ago
kcarey
• 0
0
votes
3
replies
195
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 11 days ago by
ATpoint
★ 4.1k • written 11 days ago by
james.zhang20
• 0
1
vote
3
replies
279
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 11 days ago by
angelathuynh5
• 0
0
votes
3
replies
284
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 11 days ago by
Michael Love
42k • written 12 days ago by
HAK
• 0
1
vote
1
reply
142
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
marcusn
• 0
0
votes
1
reply
127
views
putting my own expression data in deseq2
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 13 days ago by
Dev
• 0
0
votes
2
replies
152
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
13 days ago • updated 10 days ago
Aurora
• 0
0
votes
1
reply
128
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
Agung
• 0
3
votes
3
replies
256
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 14 days ago by
ATpoint
★ 4.1k • written 14 days ago by
bioinf
▴ 10
1
vote
3
replies
241
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 17 days ago by
Michael Love
42k • written 18 days ago by
JalapenoCornbread
• 0
2
votes
9
replies
410
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 17 days ago by
James W. MacDonald
65k • written 18 days ago by
Alexandre
• 0
0
votes
2
replies
221
views
PCA plot suggestions
DESeq2
PCAtools
updated 17 days ago by
Michael Love
42k • written 18 days ago by
Aaliya
• 0
0
votes
1
reply
163
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 18 days ago by
Michael Love
42k • written 19 days ago by
kcarey
• 0
1
vote
3
replies
227
views
Different Shrunk Log2FC according with reference
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
andrebolerbarros
▴ 20
1
vote
4
replies
348
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
19 days ago • updated 17 days ago
winwater0928
• 0
3
votes
1
reply
320
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 19 days ago by
Michael Love
42k • written 20 days ago by
i.sudbery
▴ 40
0
votes
8
replies
369
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 18 days ago by
swbarnes2
★ 1.4k • written 20 days ago by
Aaliya
• 0
3
votes
3
replies
236
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 20 days ago by
Michael Love
42k • written 21 days ago by
WardDeb
• 0
0
votes
1
reply
147
views
rlog transformation
DESeq2
updated 25 days ago by
Michael Love
42k • written 25 days ago by
ishij9717
• 0
0
votes
1
reply
120
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 25 days ago by
Michael Love
42k • written 25 days ago by
09191919
• 0
0
votes
4
replies
248
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
26 days ago • updated 23 days ago
lonn
• 0
1
vote
2
replies
726
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
26 days ago • updated 17 days ago
ussarizona
▴ 10
0
votes
1
reply
158
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 25 days ago by
ATpoint
★ 4.1k • written 26 days ago by
quanah.hudson
• 0
0
votes
1
reply
139
views
covariate with negative and positive values
DESeq2
updated 25 days ago by
Michael Love
42k • written 26 days ago by
Brynn
• 0
0
votes
3
replies
214
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 27 days ago by
Michael Love
42k • written 28 days ago by
andrebolerbarros
▴ 20
0
votes
4
replies
281
views
DEG with low counts
DESeq2
updated 24 days ago by
Michael Love
42k • written 29 days ago by
Rajat
• 0
0
votes
1
reply
138
views
Deseq2 Rlog transformation
DESeq2
updated 28 days ago by
ATpoint
★ 4.1k • written 29 days ago by
Sahar
• 0
1
vote
2
replies
207
views
Design Matrix within group comparison more than two groups
DESeq2
4 weeks ago
hemantcnaik
• 0
0
votes
1
reply
142
views
Bioinformatics student
Des
DESeq2
updated 4 weeks ago by
hemantcnaik
• 0 • written 4 weeks ago by
Sahar
• 0
0
votes
1
reply
190
views
DESeq2 gives an error and R crashes
DESeq2
4 weeks ago
Shefali
• 0
1
vote
2
replies
250
views
How to retrieve detailed regression results from deseq2
DESeq2
4 weeks ago • updated 24 days ago
Weiqian
▴ 10
0
votes
1
reply
182
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
Adelaide
• 0
0
votes
2
replies
180
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
joshua.mannheimer
• 0
0
votes
2
replies
233
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
nhaus
▴ 30
0
votes
2
replies
256
views
Regressing out batch effects
DESeq2
updated 4 weeks ago by
Michael Love
42k • written 5 weeks ago by
kys91240
• 0
1
vote
1
reply
180
views
DESeq2 - Missing values in count matrix
DESeq2
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Hong Thu
• 0
1
vote
6
replies
453
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
RL
• 0
1
vote
1
reply
166
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
5 weeks ago
Layal
• 0
0
votes
2
replies
180
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
5 weeks ago
michelafrancesconi8
• 0
0
votes
4
replies
278
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 5 weeks ago by
Michael Love
42k • written 5 weeks ago by
Aidan
• 0
0
votes
1
reply
171
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 6 weeks ago by
Michael Love
42k • written 6 weeks ago by
Mikushi
• 0
50 results • Page
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Comment: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
by
alex.pico
▴ 20
Hi Matthew. Happy to help. The error message you are getting is indeed not very helpful. It's just saying that the CyREST return obj "res" …
Comment: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
by
bandconductor
• 0
thanks! you have saved me so much time
Comment: Problem finding certain variables when importing a public database GSE73103
by
Guido Hooiveld
★ 3.9k
FWIW: when I would like to make use of publicly available data, I always use the website to explore which metadata is submitted to GEO (and…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
This is `blockLength=200000`, and providing `seg=seg`? It's alright that it's not identical. In the bootstrapped data, you will now have l…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Thank you, Michael. I used the script shared by you. The genomic distribution of the original and null loci looks like non-stationary. Plea…
Votes
Answer: ChipQC 'names' attribute [9] must be the same length as the vector [2]'
ChipQC 'names' attribute [9] must be the same length as the vector [2]'
A: DEXSeq time course design
using variable in design formula
differential expression for Single-cell RNAseq data using edgeR
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