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deseq2
•
reset
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
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
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 23 days ago by
Alexandre
• 0
4
votes
9
replies
234
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 2 days ago by
ATpoint
★ 4.1k • written 3 days ago by
pangtaihin
• 0
0
votes
8
replies
384
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
8
replies
488
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
2
votes
7
replies
372
views
deseq2 results
DESeq2
DifferentialExpression
rnaseqGene
DifferentialRegulation
10 days ago • updated 7 days ago
sajadahmad41454
• 0
0
votes
7
replies
447
views
DESeq filtering specific to contrasts
DESeq2
updated 28 days ago by
Michael Love
42k • written 3 months ago by
Emma
• 0
0
votes
6
replies
291
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
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
1
vote
4
replies
528
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 16 days ago
JKim
• 0
1
vote
4
replies
356
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
24 days ago • updated 22 days ago
winwater0928
• 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 28 days ago
lonn
• 0
0
votes
4
replies
292
views
DEG with low counts
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
Rajat
• 0
3
votes
3
replies
268
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 19 days ago by
ATpoint
★ 4.1k • written 19 days ago by
bioinf
▴ 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 10 days ago by
ATpoint
★ 4.1k • written 16 days ago by
angelathuynh5
• 0
3
votes
3
replies
251
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 25 days ago by
Michael Love
42k • written 25 days ago by
WardDeb
• 0
1
vote
3
replies
235
views
Different Shrunk Log2FC according with reference
DESeq2
updated 24 days ago by
Michael Love
42k • written 24 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
254
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 14 days ago by
Reza
• 0
1
vote
3
replies
253
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 22 days ago by
Michael Love
42k • written 22 days ago by
JalapenoCornbread
• 0
0
votes
3
replies
301
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
0
votes
3
replies
222
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 16 days ago by
ATpoint
★ 4.1k • written 16 days ago by
james.zhang20
• 0
0
votes
3
replies
105
views
Assymetric MA plot with no overall trend
DESeq2
DifferentialExpression
updated 3 days ago by
Michael Love
42k • written 3 days ago by
Kasper
• 0
0
votes
2
replies
161
views
DESeq2 v1.35.0
DESeq2
updated 15 days ago by
Michael Love
42k • written 15 days ago by
Espresso
• 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
2
replies
167
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
18 days ago • updated 15 days ago
Aurora
• 0
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
2
replies
227
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
740
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 21 days ago
Patadù
▴ 10
0
votes
2
replies
145
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
updated 8 hours ago by
JKim
• 0 • written 1 day ago by
Ken C
• 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 8 days ago by
maria.soler
• 0 • written 16 months ago by
kalavattam
▴ 10
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
1
vote
1
reply
185
views
Handling multiple differential expression comparisons
DESeq2
updated 13 days ago by
Michael Love
42k • written 14 days ago by
Zainab
▴ 10
0
votes
1
reply
138
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
Agung
• 0
1
vote
1
reply
155
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 18 days ago by
Michael Love
42k • written 18 days ago by
marcusn
• 0
0
votes
1
reply
125
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
09191919
• 0
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
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
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
1
reply
135
views
putting my own expression data in deseq2
DESeq2
updated 18 days ago by
ATpoint
★ 4.1k • written 18 days ago by
Dev
• 0
0
votes
1
reply
84
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
1
reply
54
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
21 hours ago • updated 20 hours ago
shaunpeterson
• 0
0
votes
1
reply
100
views
normalization using Deseq2
DESeq2
rnaseqGene
Normalization
updated 9 days ago by
ATpoint
★ 4.1k • written 9 days ago by
sajadahmad41454
• 0
0
votes
1
reply
162
views
Differential gene expression analysis results
DESeq2
DifferentialExpression
updated 8 days ago by
ATpoint
★ 4.1k • written 8 days ago by
sajadahmad41454
• 0
0
votes
1
reply
157
views
rlog transformation
DESeq2
updated 29 days ago by
Michael Love
42k • written 4 weeks ago by
ishij9717
• 0
45 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
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