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DESEq2
•
reset
1
vote
2
replies
182
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
6 days ago • updated 4 hours ago
angelathuynh5
• 0
1
vote
1
reply
107
views
Handling multiple differential expression comparisons
DESeq2
updated 2 days ago by
Michael Love
42k • written 4 days ago by
Zainab
▴ 10
2
votes
3
replies
183
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 4 days ago by
Reza
• 0
0
votes
6
replies
223
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 3 days ago by
swbarnes2
★ 1.3k • written 5 days ago by
arfranco
▴ 130
0
votes
2
replies
129
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
7 days ago • updated 4 days ago
Aurora
• 0
0
votes
2
replies
150
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
6 days ago • updated 5 days ago
kcarey
• 0
0
votes
2
replies
112
views
DESeq2 v1.35.0
DESeq2
updated 5 days ago by
Michael Love
42k • written 5 days ago by
Espresso
• 0
0
votes
3
replies
151
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 5 days ago by
ATpoint
★ 4.1k • written 6 days ago by
james.zhang20
• 0
0
votes
3
replies
258
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 6 days ago by
Michael Love
42k • written 7 days ago by
HAK
• 0
1
vote
4
replies
483
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 6 days ago
JKim
• 0
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 7 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
1
vote
1
reply
118
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 7 days ago by
Michael Love
42k • written 7 days ago by
marcusn
• 0
0
votes
1
reply
109
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 7 days ago by
Michael Love
42k • written 8 days ago by
Agung
• 0
0
votes
1
reply
113
views
putting my own expression data in deseq2
DESeq2
updated 7 days ago by
ATpoint
★ 4.1k • written 7 days ago by
Dev
• 0
3
votes
3
replies
241
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 8 days ago by
ATpoint
★ 4.1k • written 9 days ago by
bioinf
▴ 10
0
votes
2
replies
214
views
PCA plot suggestions
DESeq2
PCAtools
updated 11 days ago by
Michael Love
42k • written 13 days ago by
Aaliya
• 0
1
vote
2
replies
719
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
20 days ago • updated 11 days ago
ussarizona
▴ 10
1
vote
3
replies
227
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 11 days ago by
Michael Love
42k • written 12 days ago by
JalapenoCornbread
• 0
1
vote
4
replies
335
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
13 days ago • updated 11 days ago
winwater0928
• 0
2
votes
9
replies
394
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
Alexandre
• 0
0
votes
8
replies
356
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 12 days ago by
swbarnes2
★ 1.3k • written 14 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 13 days ago by
Michael Love
42k • written 13 days ago by
kcarey
• 0
1
vote
3
replies
216
views
Different Shrunk Log2FC according with reference
DESeq2
updated 13 days ago by
Michael Love
42k • written 13 days ago by
andrebolerbarros
▴ 20
3
votes
1
reply
316
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 14 days ago by
Michael Love
42k • written 14 days ago by
i.sudbery
▴ 40
3
votes
3
replies
231
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 14 days ago by
Michael Love
42k • written 15 days ago by
WardDeb
• 0
0
votes
4
replies
241
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
20 days ago • updated 17 days ago
lonn
• 0
1
vote
2
replies
245
views
How to retrieve detailed regression results from deseq2
DESeq2
27 days ago • updated 18 days ago
Weiqian
▴ 10
0
votes
7
replies
425
views
DESeq filtering specific to contrasts
DESeq2
updated 18 days ago by
Michael Love
42k • written 11 weeks ago by
Emma
• 0
2
votes
5
replies
757
views
DESeq2 setting significant p-value
DESeq2
updated 18 days ago by
Michael Love
42k • written 5.0 years ago by
Merlin
▴ 10
0
votes
4
replies
270
views
DEG with low counts
DESeq2
updated 18 days ago by
Michael Love
42k • written 23 days ago by
Rajat
• 0
0
votes
1
reply
139
views
rlog transformation
DESeq2
updated 19 days ago by
Michael Love
42k • written 19 days ago by
ishij9717
• 0
0
votes
1
reply
113
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 19 days ago by
Michael Love
42k • written 19 days ago by
09191919
• 0
0
votes
1
reply
135
views
covariate with negative and positive values
DESeq2
updated 19 days ago by
Michael Love
42k • written 21 days ago by
Brynn
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 19 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
0
votes
1
reply
150
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 19 days ago by
ATpoint
★ 4.1k • written 20 days ago by
quanah.hudson
• 0
2
votes
5
replies
1.2k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 20 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
4
replies
603
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 21 days ago by
Michael Love
42k • written 6 months ago by
Crystal571
• 0
0
votes
3
replies
207
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 21 days ago by
Michael Love
42k • written 22 days ago by
andrebolerbarros
▴ 20
0
votes
1
reply
133
views
Deseq2 Rlog transformation
DESeq2
updated 22 days ago by
ATpoint
★ 4.1k • written 23 days ago by
Sahar
• 0
1
vote
2
replies
199
views
Design Matrix within group comparison more than two groups
DESeq2
25 days ago • updated 24 days ago
hemantcnaik
• 0
0
votes
1
reply
137
views
Bioinformatics student
Des
DESeq2
updated 25 days ago by
hemantcnaik
• 0 • written 25 days ago by
Sahar
• 0
0
votes
1
reply
178
views
DESeq2 gives an error and R crashes
DESeq2
27 days ago • updated 26 days ago
Shefali
• 0
0
votes
2
replies
223
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
nhaus
▴ 30
0
votes
1
reply
167
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 28 days ago by
Michael Love
42k • written 28 days ago by
Adelaide
• 0
0
votes
2
replies
249
views
Regressing out batch effects
DESeq2
updated 28 days ago by
Michael Love
42k • written 4 weeks ago by
kys91240
• 0
0
votes
2
replies
173
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
joshua.mannheimer
• 0
1
vote
1
reply
170
views
DESeq2 - Missing values in count matrix
DESeq2
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Hong Thu
• 0
1
vote
6
replies
438
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 4 weeks ago by
Michael Love
42k • written 4 weeks ago by
RL
• 0
0
votes
2
replies
174
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
5 weeks ago • updated 4 weeks ago
michelafrancesconi8
• 0
1
vote
1
reply
158
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
5 weeks ago • updated 4 weeks ago
Layal
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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