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DESeq2
•
reset
5
votes
12
replies
2.1k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 1 day ago by
Seyram M.
• 0 • written 4.6 years ago by
hsbio
▴ 10
1
vote
8
replies
1.2k
views
DESeq2 test for synergistic vs additive effects
synergistic
additive
DESeq2
updated 17 days ago by
Wolfgang Huber
★ 13k • written 9 months ago by
Jane
▴ 10
4
votes
7
replies
659
views
DESeq2 unable to handle large count values
DESeq2
updated 29 days ago by
Michael Love
41k • written 5 months ago by
robennet
• 0
0
votes
7
replies
394
views
DESeq2 filtering vs edgeR filtering
DESeq2
5 weeks ago • updated 22 days ago
fr8712ca-s
• 0
1
vote
6
replies
388
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 14 days ago by
Michael Love
41k • written 14 days ago by
RL
• 0
2
votes
5
replies
1.1k
views
DESeq2 remove batch effect
BatchEffect
RNASeqData
WGCNA
DESeq2
updated 16 hours ago by
Ashley
• 0 • written 10 months ago by
zxc741xb
• 0
0
votes
4
replies
209
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 15 days ago by
Michael Love
41k • written 16 days ago by
Aidan
• 0
0
votes
4
replies
549
views
How to correct for known and surrogate variables in DESeq2?
DESeq2
BatchEffect
sva
limma
updated 1 day ago by
Michael Love
41k • written 5 months ago by
Crystal571
• 0
2
votes
3
replies
308
views
PCA of different bacterial species
DESeq2
updated 21 days ago by
Michael Love
41k • written 22 days ago by
Laura
▴ 10
0
votes
3
replies
157
views
DEG with low counts
DESeq2
3 days ago • updated 1 day ago
Rajat
• 0
0
votes
3
replies
126
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
andrebolerbarros
▴ 20
2
votes
3
replies
267
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 28 days ago by
Michael Love
41k • written 4 weeks ago by
andrebolerbarros
▴ 20
0
votes
3
replies
223
views
Help with Complex DESeq2 Design
DESeq2
updated 28 days ago by
ATpoint
★ 4.0k • written 4 weeks ago by
kelsey.beavers
• 0
1
vote
2
replies
195
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
27 days ago • updated 21 days ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
209
views
Regressing out batch effects
DESeq2
updated 8 days ago by
Michael Love
41k • written 13 days ago by
kys91240
• 0
3
votes
2
replies
185
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
23 days ago
Anita
▴ 10
0
votes
2
replies
127
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 12 days ago by
James W. MacDonald
65k • written 12 days ago by
joshua.mannheimer
• 0
0
votes
2
replies
194
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
28 days ago • updated 27 days ago
kcarey
• 0
1
vote
2
replies
144
views
Design Matrix within group comparison more than two groups
DESeq2
5 days ago • updated 4 days ago
hemantcnaik
• 0
0
votes
2
replies
175
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 8 days ago by
Michael Love
41k • written 12 days ago by
nhaus
▴ 30
0
votes
2
replies
139
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
15 days ago • updated 14 days ago
michelafrancesconi8
• 0
1
vote
1
reply
143
views
DESeq2 - Missing values in count matrix
DESeq2
updated 13 days ago by
James W. MacDonald
65k • written 13 days ago by
Hong Thu
• 0
0
votes
1
reply
137
views
DESeq2 gives an error and R crashes
DESeq2
7 days ago • updated 6 days ago
Shefali
• 0
1
vote
1
reply
152
views
How to retrieve detailed regression results from deseq2
DESeq2
updated 2 days ago by
Michael Love
41k • written 7 days ago by
Weiqian
▴ 10
0
votes
1
reply
130
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 20 days ago by
Michael Love
41k • written 20 days ago by
Mikushi
• 0
0
votes
1
reply
100
views
Bioinformatics student
Des
DESeq2
updated 5 days ago by
hemantcnaik
• 0 • written 5 days ago by
Sahar
• 0
1
vote
1
reply
124
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
15 days ago • updated 14 days ago
Layal
• 0
0
votes
1
reply
82
views
Deseq2 Rlog transformation
DESeq2
updated 2 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Sahar
• 0
0
votes
1
reply
120
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 8 days ago by
Michael Love
41k • written 8 days ago by
Adelaide
• 0
0
votes
1
reply
146
views
collapseReplicates dimension error
DESeq2
Dese
updated 23 days ago by
Michael Love
41k • written 26 days ago by
Léa
• 0
0
votes
0
replies
27
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
16 hours ago
quanah.hudson
• 0
0
votes
0
replies
25
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 hours ago • updated 12 hours ago
ussarizona
• 0
0
votes
0
replies
15
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
14 hours ago
lonn
• 0
0
votes
0
replies
40
views
covariate with negative and positive values
DESeq2
1 day ago
Brynn
• 0
34 results • Page
1 of 1
Recent ...
Replies
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma
by
Gordon Smyth
50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq
by
wichaidi
• 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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