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DESeq2
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20
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Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
45 minutes ago • updated 42 minutes ago
Alexandre
• 0
0
votes
0
replies
22
views
PCA plot suggestions
DESeq2
PCAtools
9 hours ago
Aaliya
• 0
0
votes
1
reply
70
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2
RNAseq
updated 16 hours ago by
Michael Love
41k • written 19 hours ago by
kcarey
• 0
1
vote
3
replies
84
views
Different Shrunk Log2FC according with reference
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
andrebolerbarros
▴ 20
0
votes
3
replies
92
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
updated 5 minutes ago by
James W. MacDonald
65k • written 1 day ago by
winwater0928
• 0
2
votes
1
reply
163
views
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
i.sudbery
▴ 40
0
votes
8
replies
214
views
DESeq2 output used for PCA plot on R studio
DESeq2
RSTUDIO
PCAtools
updated 7 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
Aaliya
• 0
3
votes
3
replies
155
views
DESeq2 - dispersion estimation when there is none
DESeq2
updated 1 day ago by
Michael Love
41k • written 2 days ago by
WardDeb
• 0
0
votes
1
reply
88
views
rlog transformation
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ishij9717
• 0
0
votes
1
reply
86
views
ONT long-read RNA sequencing - data analysis options
DESeq2
LongRead
DEXSeq
IsoformSwitchAnalyzeR
RNASeq
updated 6 days ago by
Michael Love
41k • written 7 days ago by
09191919
• 0
0
votes
1
reply
96
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
updated 6 days ago by
Michael Love
41k • written 7 days ago by
ussarizona
• 0
0
votes
1
reply
113
views
covariate with negative and positive values
DESeq2
updated 6 days ago by
Michael Love
41k • written 8 days ago by
Brynn
• 0
0
votes
1
reply
113
views
DESEQ2 output gives multiple groups when only 2 groups are present
DESeq2
updated 7 days ago by
ATpoint
★ 4.0k • written 8 days ago by
quanah.hudson
• 0
0
votes
4
replies
194
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
7 days ago • updated 5 days ago
lonn
• 0
0
votes
3
replies
174
views
Interaction Terms in DESeq2 - Shrinkage
DESeq2
updated 8 days ago by
Michael Love
41k • written 9 days ago by
andrebolerbarros
▴ 20
1
vote
2
replies
218
views
How to retrieve detailed regression results from deseq2
DESeq2
14 days ago • updated 5 days ago
Weiqian
▴ 10
0
votes
4
replies
229
views
DEG with low counts
DESeq2
updated 6 days ago by
Michael Love
41k • written 10 days ago by
Rajat
• 0
0
votes
1
reply
109
views
Deseq2 Rlog transformation
DESeq2
updated 10 days ago by
ATpoint
★ 4.0k • written 11 days ago by
Sahar
• 0
1
vote
2
replies
163
views
Design Matrix within group comparison more than two groups
DESeq2
12 days ago
hemantcnaik
• 0
0
votes
1
reply
117
views
Bioinformatics student
Des
DESeq2
updated 12 days ago by
hemantcnaik
• 0 • written 12 days ago by
Sahar
• 0
0
votes
1
reply
155
views
DESeq2 gives an error and R crashes
DESeq2
14 days ago • updated 13 days ago
Shefali
• 0
0
votes
2
replies
192
views
Interaction term vs grouping variable design considerations
DESeq2
DifferentialExpression
updated 15 days ago by
Michael Love
41k • written 20 days ago by
nhaus
▴ 30
0
votes
1
reply
141
views
IgG control in RIP-seq with Deseq2
DESeq2
RIP-seq
updated 15 days ago by
Michael Love
41k • written 15 days ago by
Adelaide
• 0
0
votes
2
replies
220
views
Regressing out batch effects
DESeq2
updated 15 days ago by
Michael Love
41k • written 20 days ago by
kys91240
• 0
0
votes
2
replies
142
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2
timecourse
DifferentialExpression
updated 19 days ago by
James W. MacDonald
65k • written 19 days ago by
joshua.mannheimer
• 0
1
vote
1
reply
152
views
DESeq2 - Missing values in count matrix
DESeq2
updated 20 days ago by
James W. MacDonald
65k • written 20 days ago by
Hong Thu
• 0
1
vote
6
replies
402
views
DESeq2 step-by-step Normalization then DGE separately & Normalization methods and switchability
DESeq2
Normalization
updated 21 days ago by
Michael Love
41k • written 21 days ago by
RL
• 0
1
vote
1
reply
136
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
22 days ago
Layal
• 0
0
votes
2
replies
152
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
22 days ago
michelafrancesconi8
• 0
0
votes
4
replies
229
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 22 days ago by
Michael Love
41k • written 23 days ago by
Aidan
• 0
0
votes
1
reply
142
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 27 days ago by
Michael Love
41k • written 27 days ago by
Mikushi
• 0
2
votes
3
replies
324
views
PCA of different bacterial species
DESeq2
updated 29 days ago by
Michael Love
41k • written 29 days ago by
Laura
▴ 10
0
votes
1
reply
158
views
collapseReplicates dimension error
DESeq2
Dese
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Léa
• 0
3
votes
2
replies
200
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
4 weeks ago
Anita
▴ 10
1
vote
2
replies
212
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
4 weeks ago • updated 28 days ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
210
views
Filtering and Reference Level for DESeq2
DESeq2
GeneFiltering
RNAseq
5 weeks ago • updated 4 weeks ago
kcarey
• 0
2
votes
3
replies
285
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
andrebolerbarros
▴ 20
0
votes
3
replies
243
views
Help with Complex DESeq2 Design
DESeq2
updated 5 weeks ago by
ATpoint
★ 4.0k • written 5 weeks ago by
kelsey.beavers
• 0
1
vote
1
reply
164
views
Need help with creating and plotting temporal clustering analysis of DEGs
DESeq2
ctsGE
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Emma
• 0
0
votes
1
reply
132
views
Help with DESeqDataSetFromHTSeqCount
DESeq2
RSeqAn
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
rahaf.nazzal9
• 0
0
votes
1
reply
164
views
lfcShrink error: the line search routine failed
apeglm
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Yuqin
• 0
2
votes
2
replies
207
views
With DESeq2 "Not full rank" Error with design
DESeq2
DEs
5 weeks ago
feather-W
• 0
0
votes
2
replies
302
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 6 weeks ago by
Michael Love
41k • written 6 weeks ago by
gglatzer
• 0
0
votes
4
replies
405
views
DESeq2: subtract effect of an isotope control before comparing to a baseline sample?
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 6 weeks ago by
Jad
• 0
0
votes
7
replies
407
views
DESeq2 filtering vs edgeR filtering
DESeq2
6 weeks ago • updated 29 days ago
fr8712ca-s
• 0
0
votes
2
replies
239
views
RNA sequencing raw counts gene filtering
DESeq2
limma
RNAseq
6 weeks ago • updated 5 weeks ago
kcarey
• 0
1
vote
1
reply
206
views
i'm not getting any differentially expressed genes.
DESeq2
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
Marilyn
• 0
2
votes
1
reply
233
views
Creating data matrix in Deseq2 from tximport data invalid class SummarizedExperiment object
DESeq2
tximport
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
hemantcnaik
• 0
1
vote
1
reply
195
views
Perform PCA for sample clustering using DESeq2
DESeq2
updated 6 weeks ago by
ATpoint
★ 4.0k • written 6 weeks ago by
synat.keam
• 0
0
votes
3
replies
359
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 11 weeks ago by
pl23
• 0
50 results • Page
1 of 1
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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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