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DEseq
•
reset
40
votes
44
replies
8.1k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 5.2 years ago by
Wade Davis
▴ 60 • written 5.7 years ago by
yjiangnan
▴ 10
25
votes
11
replies
6.7k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 7.2 years ago by
Simon Anders
★ 3.7k • written 7.2 years ago by
Nik Tuzov
▴ 80
24
votes
22
replies
15k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 5.6 years ago by
k.vitting.seerup
▴ 120 • written 7.4 years ago by
tangming2005
▴ 190
15
votes
5
replies
6.4k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma
voom
deseq
normalization
ercc
updated 7.2 years ago by
Gordon Smyth
47k • written 7.2 years ago by
komal.rathi
▴ 100
15
votes
8
replies
10k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2
deseq
8.2 years ago
salahm
▴ 70
14
votes
15
replies
46k
views
DESeq2 output explanation
deseq
deseq2
updated 15 months ago by
Michael Love
39k • written 8.2 years ago by
francesca.defilippis
▴ 80
14
votes
9
replies
12k
views
How does DESeq2 handle zero counts in one condition?
deseq2
deseq
rna-seq
8.1 years ago
gavrielmatt
▴ 30
13
votes
6
replies
6.1k
views
DESeq2 multiple interaction terms 3-factor design
deseq2
deseq
interactions
multiple factor design
updated 7.1 years ago by
Michael Love
39k • written 7.1 years ago by
Stephen Turner
▴ 290
10
votes
14
replies
10k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 23 months ago by
Kai_Qi
▴ 20 • written 7.0 years ago by
Giard
▴ 30
10
votes
14
replies
2.9k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma
edger
deseq
deseq2
updated 5.4 years ago by
Gordon Smyth
47k • written 5.4 years ago by
Nik Tuzov
▴ 80
9
votes
17
replies
1.1k
views
DESeq2 design subcategories
deseq2
deseq
differential binding analysis
updated 5.2 years ago by
Michael Love
39k • written 5.2 years ago by
rbronste
▴ 60
9
votes
6
replies
7.5k
views
Error bars DESeq or DESeq2 fold change
rnaseq
deseq2
deseq
standard error
confidence interval
updated 15 months ago by
Michael Love
39k • written 6.8 years ago by
lisa.crossman
▴ 10
8
votes
2
replies
2.2k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts
proteomics
limma
edger
deseq
updated 7.6 years ago by
Gordon Smyth
47k • written 7.6 years ago by
eleonoregravier
▴ 60
8
votes
4
replies
1.6k
views
DESeq2: interaction term as in limma
deseq2
deseq
limma
interaction term
updated 5.8 years ago by
Simon Anders
★ 3.7k • written 5.8 years ago by
sbcn
▴ 80
7
votes
12
replies
8.2k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2
deseq
updated 5.7 years ago by
bio2001
▴ 60 • written 8.3 years ago by
skyoflcz
▴ 20
7
votes
3
replies
3.4k
views
DESeq2 with interaction using SVA
deseq2
sva
interaction term
grouping variable
deseq
5.0 years ago
kevin.kingsland
▴ 60
6
votes
12
replies
13k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2
deseq
counts
rnaseq
differential gene expression
updated 6.8 years ago by
Michael Love
39k • written 6.8 years ago by
wannes.nauwynck
▴ 10
6
votes
7
replies
3.1k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq
deseq
7.2 years ago
tonja.r
▴ 80
5
votes
11
replies
23k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 8.0 years ago by
Michael Love
39k • written 8.0 years ago by
c.lieftink@nki.nl
▴ 30
5
votes
2
replies
1.1k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq
deseq2
vst
updated 5.8 years ago by
Wolfgang Huber
13k • written 5.8 years ago by
jiab
• 0
5
votes
3
replies
6.3k
views
What problem does the MA plot diagnose? And how do you solve it?
deseq2
deseq
rnaseq
updated 5.9 years ago by
Ryan C. Thompson
7.8k • written 5.9 years ago by
ysdel
▴ 40
5
votes
13
replies
4.5k
views
P values from Deseq Analysis
deseq
5.8 years ago • updated 5.7 years ago
Shrikant Pawar
• 0
5
votes
18
replies
6.6k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
7.4 years ago
Radek
▴ 90
4
votes
7
replies
2.4k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 4.3 years ago by
Michael Love
39k • written 4.3 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
4.5 years ago
ansari.sarabio
• 0
4
votes
6
replies
925
views
DESeq2 design and stats question
deseq2
differential binding analysis
deseq
atac-seq
updated 5.0 years ago by
Michael Love
39k • written 5.0 years ago by
rbronste
▴ 60
4
votes
4
replies
2.3k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 3.5 years ago by
wunderl
▴ 30 • written 3.5 years ago by
neekonsu
• 0
4
votes
3
replies
2.6k
views
Add new columns to DESeqResults from text file by matching rownames.
deseq2
deseq
merge data frames
cbind
s4vectors
updated 5.4 years ago by
Michael Love
39k • written 5.4 years ago by
kirannbishwa01
• 0
4
votes
2
replies
7.2k
views
Analyzing RNA-Seq data without replicates using DESeq
deseq
DESeq2
updated 8.4 years ago by
Michael Love
39k • written 8.4 years ago by
solgakar@bi.technion.ac.il
▴ 90
4
votes
7
replies
909
views
Filtering DESeq2 result export along multiple lines
deseq2
differential binding analysis
deseq
updated 5.2 years ago by
Michael Love
39k • written 5.2 years ago by
rbronste
▴ 60
4
votes
3
replies
2.3k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger
deseq
deseq2
5.7 years ago
michael.steffen
▴ 20
4
votes
14
replies
13k
views
standard error value (lfcSE) returned by DeSeq2
deseq2
deseq
lfc
lfcse
standard error
updated 5.8 years ago by
rraadd_8
• 0 • written 5.9 years ago by
tootiki
• 0
4
votes
6
replies
871
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
16 months ago
s-rhussien
• 0
3
votes
4
replies
2.7k
views
Variance filtering prior to RNA-seq differential expression
sequencing
deseq
limma
updated 7.6 years ago by
Gordon Smyth
47k • written 7.6 years ago by
chris86
▴ 400
3
votes
7
replies
717
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2
deseq
4.5 years ago
blastzone.heimerdinger
▴ 10
3
votes
12
replies
925
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
4.0 years ago
ariel
▴ 10
3
votes
5
replies
5.7k
views
DESeq2 resultsNames output
deseq
deseq2
updated 8.0 years ago by
Michael Love
39k • written 8.0 years ago by
igor
▴ 40
3
votes
3
replies
1.5k
views
read counts of paired end reads for DESeq2 analysis
deseq
featurecounts
paired
updated 6.8 years ago by
Steve Lianoglou
13k • written 6.8 years ago by
tszn1984
• 0
3
votes
14
replies
16k
views
Normalization in DESeq2
deseq2
deseq
updated 8.2 years ago by
Michael Love
39k • written 8.2 years ago by
solgakar@bi.technion.ac.il
▴ 90
3
votes
4
replies
2.7k
views
DESeq is better than DESeq2?
deseq2
deseq
6.9 years ago
ribioinfo
▴ 100
3
votes
7
replies
1.6k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 4.8 years ago by
Peter Langfelder
★ 2.7k • written 4.8 years ago by
7kemZmani
▴ 10
3
votes
11
replies
2.6k
views
DESeq function taking too long
deseq2
deseq
factor
rnaseq
updated 5.5 years ago by
Peter Langfelder
★ 2.7k • written 5.5 years ago by
sup230
▴ 30
3
votes
8
replies
3.6k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing
DESeq
Sequencing
DESeq
updated 6.5 years ago by
contactbiostructure
• 0 • written 9.1 years ago by
Guest User
★ 12k
3
votes
1
reply
978
views
RNASeq testing for differential expression in one condition, equality in another (using DESeq)
deseq2
deseq
rnaseq
5.9 years ago
ysdel
▴ 40
3
votes
2
replies
10k
views
how to get normalized counts from edgeR
DESeq
DESeq
updated 10.6 years ago by
Mark Robinson
▴ 880 • written 10.6 years ago by
wang peter
★ 2.0k
3
votes
5
replies
1.9k
views
DESeq on transcripts v/s genes
DESeq
DESeq
updated 11.0 years ago by
Wolfgang Huber
13k • written 11.0 years ago by
Abhishek Pratap
▴ 410
3
votes
5
replies
2.4k
views
Using DESeq2: experimental design and extracting results
DESeq
DESeq2
DESeq
DESeq2
updated 8.7 years ago by
Michael Love
39k • written 8.7 years ago by
bio2001
▴ 60
3
votes
2
replies
2.6k
views
Nanostring ncounterdata - DESeq
RNASeq
Normalization
Preprocessing
DESeq
RNASeq
Normalization
Preprocessing
DESeq
updated 11.5 years ago by
Simon Anders
★ 3.7k • written 11.5 years ago by
Vanessa Vermeirssen
▴ 20
3
votes
5
replies
4.0k
views
Labeling points with hgnc symbols on the MA plot in DESeq2
deseq
MA
updated 6.5 years ago by
phil.chapman
▴ 150 • written 6.5 years ago by
spark27
• 0
3
votes
5
replies
734
views
Help with multi-factor Deseq analysis
deseq2
rnaseq
deseq
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
MAPK
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: TCGA: clinical data and expression data
by
sharifnstu1203002m
• 0
Hello, I am in the same problem. I downloaded "transcriptome profiling" data of TCGA by using the Bioconductor package. I get my gene expr…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
by
Jonathan Göke
▴ 40
Great to hear that you are using Bambu. Yes, I think that part of your question does not have one correct answer, there are many ways in wh…
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
by
Gordon Smyth
47k
Choosing which samples to normalize together is not dependent on library size but rather on (1) whether the tissue samples are comparable a…
Comment: Atena package - error (new user)
by
lalanis1
• 0
Thanks a lot, Calvo. Will run my files with revised version soon! Best regards, Lalani
Comment: Nested paired design with covariates in limma
by
Gordon Smyth
47k
Please post a new question with enough detail to answer your question. If you want bespoke advance, then you need to post the details of yo…
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Answer: Library sizes of miRNA sequencing data and TMM normalization with Edge-R
C: Can't install TopmedPipeline Package
Comment: Question about GWASTools gdsSubset
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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