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DEseq
•
reset
40
votes
44
replies
7.3k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 4.4 years ago by
Wade Davis
▴ 60 • written 5.0 years ago by
yjiangnan
▴ 10
25
votes
11
replies
6.2k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 6.5 years ago by
Simon Anders
★ 3.7k • written 6.5 years ago by
Nik Tuzov
▴ 70
24
votes
22
replies
13k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 4.9 years ago by
k.vitting.seerup
▴ 100 • written 6.7 years ago by
tangming2005
▴ 190
15
votes
5
replies
5.8k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma
voom
deseq
normalization
ercc
updated 6.5 years ago by
Gordon Smyth
45k • written 6.5 years ago by
komal.rathi
▴ 100
15
votes
8
replies
9.7k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2
deseq
7.5 years ago
salahm
▴ 70
14
votes
15
replies
39k
views
DESeq2 output explanation
deseq
deseq2
updated 6 months ago by
Michael Love
36k • written 7.5 years ago by
francesca.defilippis
▴ 80
11
votes
9
replies
10k
views
How does DESeq2 handle zero counts in one condition?
deseq2
deseq
rna-seq
7.4 years ago
gavrielmatt
▴ 10
10
votes
14
replies
9.4k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 14 months ago by
Kai_Qi
▴ 20 • written 6.3 years ago by
Giard
▴ 30
10
votes
14
replies
2.5k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma
edger
deseq
deseq2
updated 4.7 years ago by
Gordon Smyth
45k • written 4.7 years ago by
Nik Tuzov
▴ 70
9
votes
6
replies
5.5k
views
DESeq2 multiple interaction terms 3-factor design
deseq2
deseq
interactions
multiple factor design
updated 6.4 years ago by
Michael Love
36k • written 6.4 years ago by
Stephen Turner
▴ 270
9
votes
17
replies
888
views
DESeq2 design subcategories
deseq2
deseq
differential binding analysis
updated 4.4 years ago by
Michael Love
36k • written 4.4 years ago by
rbronste
▴ 60
9
votes
6
replies
6.2k
views
Error bars DESeq or DESeq2 fold change
rnaseq
deseq2
deseq
standard error
confidence interval
updated 6 months ago by
Michael Love
36k • written 6.1 years ago by
lisa.crossman
▴ 10
8
votes
4
replies
1.4k
views
DESeq2: interaction term as in limma
deseq2
deseq
limma
interaction term
updated 5.1 years ago by
Simon Anders
★ 3.7k • written 5.1 years ago by
sbcn
▴ 70
8
votes
2
replies
1.9k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts
proteomics
limma
edger
deseq
updated 6.9 years ago by
Gordon Smyth
45k • written 6.9 years ago by
eleonoregravier
▴ 60
7
votes
3
replies
2.9k
views
DESeq2 with interaction using SVA
deseq2
sva
interaction term
grouping variable
deseq
4.3 years ago
kevin.kingsland
▴ 60
7
votes
12
replies
7.9k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2
deseq
updated 5.0 years ago by
bio2001
▴ 60 • written 7.6 years ago by
skyoflcz
▴ 20
6
votes
12
replies
10k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2
deseq
counts
rnaseq
differential gene expression
updated 6.1 years ago by
Michael Love
36k • written 6.1 years ago by
wannes.nauwynck
▴ 10
6
votes
7
replies
2.8k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq
deseq
6.5 years ago
tonja.r
▴ 60
5
votes
2
replies
967
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq
deseq2
vst
updated 5.1 years ago by
Wolfgang Huber
13k • written 5.1 years ago by
jiab
• 0
5
votes
3
replies
6.0k
views
What problem does the MA plot diagnose? And how do you solve it?
deseq2
deseq
rnaseq
updated 5.2 years ago by
Ryan C. Thompson
7.8k • written 5.2 years ago by
ysdel
▴ 40
5
votes
18
replies
6.1k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
6.7 years ago • updated 6.6 years ago
Radek
▴ 90
5
votes
13
replies
3.7k
views
P values from Deseq Analysis
deseq
5.0 years ago
Shrikant Pawar
• 0
4
votes
7
replies
2.0k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 3.6 years ago by
Michael Love
36k • written 3.6 years ago by
thindmarsmission
• 0
4
votes
1
reply
13k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R
deseq
tcgabiolinks
3.7 years ago
ansari.sarabio
• 0
4
votes
4
replies
1.5k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 2.8 years ago by
wunderl
▴ 30 • written 2.8 years ago by
neekonsu
• 0
4
votes
6
replies
793
views
DESeq2 design and stats question
deseq2
differential binding analysis
deseq
atac-seq
updated 4.3 years ago by
Michael Love
36k • written 4.3 years ago by
rbronste
▴ 60
4
votes
3
replies
2.3k
views
Add new columns to DESeqResults from text file by matching rownames.
deseq2
deseq
merge data frames
cbind
s4vectors
updated 4.6 years ago by
Michael Love
36k • written 4.6 years ago by
kirannbishwa01
• 0
4
votes
7
replies
758
views
Filtering DESeq2 result export along multiple lines
deseq2
differential binding analysis
deseq
updated 4.5 years ago by
Michael Love
36k • written 4.5 years ago by
rbronste
▴ 60
4
votes
3
replies
2.2k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger
deseq
deseq2
4.9 years ago
michael.steffen
▴ 20
4
votes
2
replies
7.0k
views
Analyzing RNA-Seq data without replicates using DESeq
deseq
DESeq2
updated 7.7 years ago by
Michael Love
36k • written 7.7 years ago by
solgakar@bi.technion.ac.il
▴ 70
4
votes
14
replies
9.9k
views
standard error value (lfcSE) returned by DeSeq2
deseq2
deseq
lfc
lfcse
standard error
updated 5.1 years ago by
rraadd_8
• 0 • written 5.2 years ago by
tootiki
• 0
4
votes
11
replies
21k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 7.3 years ago by
Michael Love
36k • written 7.3 years ago by
c.lieftink@nki.nl
▴ 20
4
votes
6
replies
511
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
7 months ago
s-rhussien
• 0
3
votes
4
replies
2.5k
views
Variance filtering prior to RNA-seq differential expression
sequencing
deseq
limma
updated 6.8 years ago by
Gordon Smyth
45k • written 6.8 years ago by
chris86
▴ 400
3
votes
12
replies
748
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
3.2 years ago
ariel
▴ 10
3
votes
5
replies
3.5k
views
Labeling points with hgnc symbols on the MA plot in DESeq2
deseq
MA
updated 5.8 years ago by
phil.chapman
▴ 150 • written 5.8 years ago by
spark27
• 0
3
votes
3
replies
1.3k
views
read counts of paired end reads for DESeq2 analysis
deseq
featurecounts
paired
updated 6.1 years ago by
Steve Lianoglou
13k • written 6.1 years ago by
tszn1984
• 0
3
votes
5
replies
4.8k
views
DESeq2 resultsNames output
deseq
deseq2
updated 7.3 years ago by
Michael Love
36k • written 7.3 years ago by
igor
▴ 40
3
votes
14
replies
16k
views
Normalization in DESeq2
deseq2
deseq
updated 7.4 years ago by
Michael Love
36k • written 7.4 years ago by
solgakar@bi.technion.ac.il
▴ 70
3
votes
7
replies
594
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2
deseq
3.8 years ago
blastzone.heimerdinger
▴ 10
3
votes
5
replies
536
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq
rna-seq
filtering
DE
deseq2
updated 2.1 years ago by
Michael Love
36k • written 2.1 years ago by
svlachavas
▴ 780
3
votes
11
replies
2.3k
views
DESeq function taking too long
deseq2
deseq
factor
rnaseq
updated 4.8 years ago by
Peter Langfelder
★ 2.6k • written 4.8 years ago by
sup230
▴ 30
3
votes
4
replies
2.6k
views
DESeq is better than DESeq2?
deseq2
deseq
6.1 years ago
ribioinfo
▴ 100
3
votes
8
replies
3.2k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing
DESeq
Sequencing
DESeq
updated 5.7 years ago by
contactbiostructure
• 0 • written 8.4 years ago by
Guest User
★ 12k
3
votes
1
reply
878
views
RNASeq testing for differential expression in one condition, equality in another (using DESeq)
deseq2
deseq
rnaseq
5.2 years ago
ysdel
▴ 40
3
votes
5
replies
2.3k
views
Using DESeq2: experimental design and extracting results
DESeq
DESeq2
DESeq
DESeq2
updated 8.0 years ago by
Michael Love
36k • written 8.0 years ago by
bio2001
▴ 60
3
votes
5
replies
1.7k
views
DESeq on transcripts v/s genes
DESeq
DESeq
updated 10.3 years ago by
Wolfgang Huber
13k • written 10.3 years ago by
Abhishek Pratap
▴ 410
3
votes
2
replies
2.4k
views
Nanostring ncounterdata - DESeq
RNASeq
Normalization
Preprocessing
DESeq
RNASeq
Normalization
Preprocessing
DESeq
updated 10.8 years ago by
Simon Anders
★ 3.7k • written 10.8 years ago by
Vanessa Vermeirssen
▴ 20
3
votes
5
replies
634
views
Help with multi-factor Deseq analysis
deseq2
rnaseq
deseq
updated 3.7 years ago by
Michael Love
36k • written 3.7 years ago by
MAPK
• 0
3
votes
7
replies
1.3k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 4.1 years ago by
Peter Langfelder
★ 2.6k • written 4.1 years ago by
7kemZmani
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
andrebolerbarros
▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
36k
So the way the p-values are generated (non-parametric) you won't get a ranking among these that are highly significant. You can use logFC. …
Answer: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
Michael Love
36k
Note sure why it's having difficulty converging. You could use apeglm?
Comment: performing the differential binding in ChIP-seq
by
ATpoint
★ 1.2k
Cross-posted https://www.biostars.org/p/9524012/#9524012
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
Yes, i tried that. I used salmon bootstraps also for the same RNAseq data to run Swish and performed the Differential transcript expressio…
Votes
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
Answer: How to best visualize multi-level transcriptomics experiment data?
A: Interpreting results of sample-to-sample PCA/clustering and changing assignment
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