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deseq2
•
reset
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 5 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 17 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
2
votes
9
replies
388
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 10 days ago by
James W. MacDonald
65k • written 10 days ago by
Alexandre
• 0
0
votes
8
replies
342
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 10 days ago by
swbarnes2
★ 1.3k • written 12 days ago by
Aaliya
• 0
0
votes
7
replies
422
views
DESeq filtering specific to contrasts
DESeq2
updated 16 days ago by
Michael Love
41k • written 11 weeks ago by
Emma
• 0
0
votes
6
replies
188
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 1 day ago by
swbarnes2
★ 1.3k • written 3 days ago by
arfranco
▴ 130
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 18 days ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
2
votes
5
replies
746
views
DESeq2 setting significant p-value
DESeq2
updated 16 days ago by
Michael Love
41k • written 5.0 years ago by
Merlin
▴ 10
1
vote
4
replies
478
views
DEseq2 coefficient
DESeq2
coefficient
10 weeks ago • updated 4 days ago
JKim
• 0
0
votes
4
replies
235
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
18 days ago • updated 15 days ago
lonn
• 0
1
vote
4
replies
319
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
11 days ago • updated 9 days ago
winwater0928
• 0
0
votes
4
replies
269
views
DEG with low counts
DESeq2
updated 16 days ago by
Michael Love
41k • written 21 days ago by
Rajat
• 0
0
votes
4
replies
601
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 19 days ago by
Michael Love
41k • written 6 months ago by
Crystal571
• 0
3
votes
3
replies
227
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 12 days ago by
Michael Love
41k • written 13 days ago by
WardDeb
• 0
1
vote
3
replies
208
views
Different Shrunk Log2FC according with reference
DESeq2
updated 11 days ago by
Michael Love
41k • written 11 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
242
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 4 days ago by
Michael Love
41k • written 5 days ago by
HAK
• 0
3
votes
3
replies
223
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 6 days ago by
ATpoint
★ 4.1k • written 6 days ago by
bioinf
▴ 10
0
votes
3
replies
204
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 19 days ago by
Michael Love
41k • written 20 days ago by
andrebolerbarros
▴ 20
1
vote
3
replies
214
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 9 days ago by
Michael Love
41k • written 10 days ago by
JalapenoCornbread
• 0
2
votes
3
replies
150
views
Too many significant genes when integrating gtex and tcga
RNA-seq
DESeq2
updated 14 hours ago by
ATpoint
★ 4.1k • written 2 days ago by
Reza
• 0
0
votes
3
replies
129
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 3 days ago by
ATpoint
★ 4.1k • written 4 days ago by
james.zhang20
• 0
0
votes
2
replies
92
views
DESeq2 v1.35.0
DESeq2
updated 3 days ago by
Michael Love
41k • written 3 days ago by
Espresso
• 0
1
vote
2
replies
241
views
How to retrieve detailed regression results from deseq2
DESeq2
25 days ago • updated 16 days ago
Weiqian
▴ 10
1
vote
2
replies
710
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
18 days ago • updated 9 days ago
ussarizona
▴ 10
0
votes
2
replies
247
views
Regressing out batch effects
DESeq2
updated 26 days ago by
Michael Love
41k • written 4 weeks ago by
kys91240
• 0
0
votes
2
replies
204
views
PCA plot suggestions
DESeq2
PCAtools
updated 9 days ago by
Michael Love
41k • written 10 days ago by
Aaliya
• 0
1
vote
2
replies
193
views
Design Matrix within group comparison more than two groups
DESeq2
23 days ago • updated 22 days ago
hemantcnaik
• 0
0
votes
2
replies
119
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
5 days ago • updated 2 days ago
Aurora
• 0
0
votes
2
replies
220
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 25 days ago by
Michael Love
41k • written 4 weeks ago by
nhaus
▴ 30
0
votes
2
replies
125
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
4 days ago • updated 3 days ago
kcarey
• 0
0
votes
1
reply
132
views
Bioinformatics student
Des
DESeq2
updated 23 days ago by
hemantcnaik
• 0 • written 23 days ago by
Sahar
• 0
1
vote
1
reply
69
views
Handling multiple differential expression comparisons
DESeq2
updated 12 hours ago by
Michael Love
41k • written 2 days ago by
Zainab
▴ 10
0
votes
1
reply
147
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 17 days ago by
ATpoint
★ 4.1k • written 18 days ago by
quanah.hudson
• 0
0
votes
1
reply
133
views
covariate with negative and positive values
DESeq2
updated 17 days ago by
Michael Love
41k • written 19 days ago by
Brynn
• 0
0
votes
1
reply
162
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 26 days ago by
Michael Love
41k • written 26 days ago by
Adelaide
• 0
0
votes
1
reply
175
views
DESeq2 gives an error and R crashes
DESeq2
25 days ago • updated 24 days ago
Shefali
• 0
0
votes
1
reply
100
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 5 days ago by
Michael Love
41k • written 6 days ago by
Agung
• 0
0
votes
1
reply
130
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 4 days ago by
ATpoint
★ 4.1k • written 4 days ago by
angelathuynh5
• 0
0
votes
1
reply
100
views
putting my own expression data in deseq2
DESeq2
updated 5 days ago by
ATpoint
★ 4.1k • written 5 days ago by
Dev
• 0
1
vote
1
reply
102
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 5 days ago by
Michael Love
41k • written 5 days ago by
marcusn
• 0
3
votes
1
reply
309
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 11 days ago by
Michael Love
41k • written 12 days ago by
i.sudbery
▴ 40
0
votes
1
reply
136
views
rlog transformation
DESeq2
updated 17 days ago by
Michael Love
41k • written 17 days ago by
ishij9717
• 0
0
votes
1
reply
151
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 11 days ago by
Michael Love
41k • written 11 days ago by
kcarey
• 0
0
votes
1
reply
130
views
Deseq2 Rlog transformation
DESeq2
updated 20 days ago by
ATpoint
★ 4.1k • written 21 days ago by
Sahar
• 0
0
votes
1
reply
112
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 17 days ago by
Michael Love
41k • written 17 days ago by
09191919
• 0
45 results • Page
1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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