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DESEQ2
•
reset
3
votes
12
replies
2.4k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
6.8 years ago
ariel
▴ 20
0
votes
1
reply
999
views
Local versus parametric fitType in DESeq2 in this instance?
deseq2
rna-seq
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
rebeliscu
• 0
0
votes
6
replies
2.6k
views
[deseq2] normalization between samples after merging transcripts into genes
deseq2
tximport
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
marie
• 0
0
votes
5
replies
2.1k
views
Hill shape p-value histogram after differential miRNA expression analysis with DESeq2
deseq2
mirna
fdrtool
updated 6.8 years ago by
Robert Castelo
★ 3.4k • written 6.8 years ago by
L_K
• 0
5
votes
6
replies
2.2k
views
DESeq2 w. pathway/network info as a prior knowledge
deseq2
pathway
ihw
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
guidobarzaghi
▴ 20
0
votes
1
reply
1.4k
views
Deseq2 padjusted values versus pvalue
deseq2
RNASeq
padjusted
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
tanyabioinfo
▴ 30
3
votes
3
replies
1.2k
views
clarification of time-series analysis
deseq2
baseline
LRT
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
10
replies
4.0k
views
Time-series analysis with DESeq2
deseq2
time-series
design matrix
edger
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
3
replies
4.4k
views
Differences in contrast results while using DESeq2 for one vs all rest combined conditions
deseq2
rna-seq
differential expression analysis
6.8 years ago
shreygandhi1990
▴ 10
1
vote
3
replies
2.9k
views
Using RUVSeq RUVs() to perform batch correction using technical replicates
RUVSeq
ruvseq
RUVs
DESEq2
deseq2
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
enricoferrero
▴ 680
0
votes
6
replies
1.4k
views
DESeq2:varianceStabilizingTransformation suggested. Results suspicious
deseq2
6.8 years ago
jovel_juan
▴ 30
1
vote
2
replies
1.8k
views
DESeq2: RNA-Seq time series analysis after removal of batch effect
deseq2
time series
remove batch effect
6.8 years ago
Nicola
• 0
4
votes
4
replies
3.1k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2
ruvseq
sva
edger
limma
updated 6.8 years ago by
Gordon Smyth
53k • written 6.8 years ago by
enricoferrero
▴ 680
2
votes
1
reply
1.2k
views
tximport: question concerning 'bias corrected counts without an offset' method
tximport
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
Thomas Bradley
• 0
8
votes
4
replies
3.3k
views
edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin
edgeR
deseq2
normalization
rnaseq
updated 6.8 years ago by
Ryan C. Thompson
★ 7.9k • written 6.8 years ago by
aec
▴ 90
0
votes
1
reply
1000
views
Data filtering in DESeq2
deseq2
data filtering
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
sally.badawi
• 0
0
votes
5
replies
865
views
DESeq2 overestimates log2Fold Change
deseq2
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
marcomhefti
• 0
0
votes
1
reply
1.1k
views
differentail expression analysis with interaction terms
edger
deseq2
interaction
design matrix
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
2.2k
views
Summary results interpretation in DeSeq2
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
sharmila.ahmad
• 0
8
votes
2
replies
1.4k
views
Does IHW use the supplied alpha for the correction calculations?
IHW
deseq2
updated 6.8 years ago by
Nikos Ignatiadis
▴ 180 • written 6.8 years ago by
k.vitting.seerup
▴ 120
0
votes
6
replies
1.9k
views
DESeq2: paired samples + controls
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
guidobarzaghi
▴ 20
6
votes
7
replies
2.4k
views
DESeq2: 5 Conditions (B vs C) vs (D vs B)
deseq2
contrast
ratio of ratio
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
Fischer-philipp
▴ 30
1
vote
1
reply
1.5k
views
design for DEseq2: LRT vs Wald & interactions
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
cintapq
▴ 10
1
vote
3
replies
1.6k
views
Appropriate design formula for DESeq2 from principles
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
galen.seilis
• 0
0
votes
2
replies
6.8k
views
[Resolved] RcppArmadillo pckg ERRORS : non-zero exit status (and so DESeq2 also)
DESEq2
R
linux
RcppArmadillo
6.8 years ago
RS1
• 0
0
votes
1
reply
3.9k
views
basemean cut off in DESEQ2
deseq2
6.8 years ago
angajalaanusha
▴ 10
0
votes
6
replies
2.1k
views
stringasfactor = F changes the output of pheatmap, why?
deseq2
pheatmap
updated 6.8 years ago by
Wolfgang Huber
★ 13k • written 6.8 years ago by
bdy8
▴ 10
2
votes
3
replies
923
views
Recommendations for normalisation post-deseq2
deseq2
normalization
posthoc
6.8 years ago
marc.osullivan
• 0
1
vote
1
reply
1.1k
views
Normalized counts from DESeq2 results in similar but not equal total read count?
deseq2
normalization
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
ricardo3889
• 0
1
vote
8
replies
1.1k
views
DEseq2 - design help
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
udp3f
• 0
1
vote
2
replies
795
views
RESULTS() using contrast=c("condition","A","B"), the results would be A vs B correct?
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
angajalaanusha
▴ 10
0
votes
3
replies
1.0k
views
DESeq: Design model for paired design with two treatments
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
L_K
• 0
4
votes
6
replies
4.8k
views
DESeq2::sizeFactors() function does not output the sizeFactor table.
deseq2
updated 21 months ago by
Dinesh
• 0 • written 6.8 years ago by
Ben
▴ 50
2
votes
1
reply
737
views
NAs create inaccuracies with BH corrections in deseq2
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
marc.osullivan
• 0
0
votes
1
reply
927
views
Paired samples in DESeq2
R
deseq2
Paired
Samples
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
m.wekking
• 0
1
vote
1
reply
637
views
Script for fold change in DESeq for count data with 2 groups
deseq2
RNAseq
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
marc.osullivan
• 0
0
votes
1
reply
628
views
Deseq2 two controls in design experiment
Deseq2
RNASeq
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
tanyabioinfo
▴ 30
0
votes
9
replies
17k
views
How to generate a volcano plot when p-values from DESeq2 are zero?
deseq2
pvalue
visualization
enhancedvolcano
rnaseq
written 6.8 years ago by
ricardo3889
• 0
0
votes
2
replies
707
views
Error in checkFullRank(modelMatrix) :
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
sharmila.ahmad
• 0
0
votes
2
replies
3.5k
views
DESEq2 rownames: NULL
deseq2
R
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
ayang
• 0
0
votes
3
replies
867
views
How to specify contrasts in DESeqDataSetFromMatrix
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
florian.dufey
• 0
3
votes
1
reply
538
views
Detect genes that moved up or down over time in the same way in multiple strains, DESeq2
deseq2
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
huganye
• 0
0
votes
1
reply
2.5k
views
Low basemean and extremely high log2FC values, DESeq2
deseq2
interpretation
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
g.wang2
• 0
0
votes
1
reply
1.2k
views
Highly uneven mapping rates and counts between samples
limma
normalization
deseq2
updated 6.8 years ago by
Aaron Lun
★ 29k • written 6.8 years ago by
chris86
▴ 420
0
votes
1
reply
844
views
DESeq2 3 factor design - whether to split up data or add interaction terms
deseq2
design
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
atongz652
• 0
0
votes
2
replies
2.1k
views
DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2
design
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
bioinfo
• 0
0
votes
3
replies
946
views
Comparison of DESeq2 and BNB-R model
DESeq2
BNB-R
updated 6.8 years ago by
Michael Love
43k • written 6.8 years ago by
Homer
• 0
1
vote
3
replies
816
views
How to create 3 way interactions model for Deseq
deseq2
6.8 years ago
sharmila.ahmad
• 0
0
votes
0
replies
756
views
diffbind: use of continuous variables
diffbind
deseq2
6.8 years ago
janani.sundaresan
• 0
1
vote
4
replies
3.1k
views
Cannot install DESeq2
deseq2
updated 6.8 years ago by
Mike Smith
★ 6.6k • written 6.8 years ago by
mhz
• 0
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