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DEseq
•
reset
40
votes
44
replies
9.2k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 5.8 years ago by
Wade Davis
▴ 60 • written 6.4 years ago by
yjiangnan
▴ 10
26
votes
22
replies
17k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 6.2 years ago by
k.vitting.seerup
▴ 120 • written 8.0 years ago by
tangming2005
▴ 190
25
votes
11
replies
7.2k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 7.8 years ago by
Simon Anders
★ 3.7k • written 7.9 years ago by
Nik Tuzov
▴ 80
17
votes
15
replies
53k
views
DESeq2 output explanation
deseq
deseq2
updated 22 months ago by
Michael Love
40k • written 8.9 years ago by
francesca.defilippis
▴ 100
16
votes
5
replies
6.9k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma
voom
deseq
normalization
ercc
updated 7.8 years ago by
Gordon Smyth
48k • written 7.8 years ago by
komal.rathi
▴ 110
15
votes
8
replies
10k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2
deseq
8.9 years ago
salahm
▴ 70
14
votes
9
replies
13k
views
How does DESeq2 handle zero counts in one condition?
deseq2
deseq
rna-seq
8.7 years ago
gavrielmatt
▴ 30
13
votes
6
replies
6.6k
views
DESeq2 multiple interaction terms 3-factor design
deseq2
deseq
interactions
multiple factor design
updated 7.7 years ago by
Michael Love
40k • written 7.7 years ago by
Stephen Turner
▴ 290
10
votes
14
replies
3.6k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma
edger
deseq
deseq2
updated 6.0 years ago by
Gordon Smyth
48k • written 6.0 years ago by
Nik Tuzov
▴ 80
10
votes
14
replies
11k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 2.5 years ago by
Kai_Qi
▴ 20 • written 7.6 years ago by
Giard
▴ 30
9
votes
6
replies
8.9k
views
Error bars DESeq or DESeq2 fold change
rnaseq
deseq2
deseq
standard error
confidence interval
updated 22 months ago by
Michael Love
40k • written 7.5 years ago by
lisa.crossman
▴ 10
9
votes
17
replies
1.4k
views
DESeq2 design subcategories
deseq2
deseq
differential binding analysis
updated 5.8 years ago by
Michael Love
40k • written 5.8 years ago by
rbronste
▴ 60
8
votes
4
replies
1.8k
views
DESeq2: interaction term as in limma
deseq2
deseq
limma
interaction term
updated 6.4 years ago by
Simon Anders
★ 3.7k • written 6.4 years ago by
sbcn
▴ 80
8
votes
3
replies
4.0k
views
DESeq2 with interaction using SVA
deseq2
sva
interaction term
grouping variable
deseq
5.7 years ago
kevin.kingsland
▴ 70
8
votes
2
replies
2.5k
views
Statistical analysis of Spectral count data : edgeR, limma or others ?
spectral counts
proteomics
limma
edger
deseq
updated 8.2 years ago by
Gordon Smyth
48k • written 8.2 years ago by
eleonoregravier
▴ 60
7
votes
12
replies
8.5k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2
deseq
updated 6.3 years ago by
bio2001
▴ 60 • written 8.9 years ago by
skyoflcz
▴ 20
7
votes
18
replies
7.5k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
8.0 years ago
Radek
▴ 90
6
votes
12
replies
15k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2
deseq
counts
rnaseq
differential gene expression
updated 7.4 years ago by
Michael Love
40k • written 7.4 years ago by
wannes.nauwynck
▴ 10
6
votes
7
replies
3.5k
views
RUVseq PCA on raw data, whereas DESeq suggests stabilization
ruvseq
deseq
7.8 years ago
tonja.r
▴ 80
5
votes
11
replies
25k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 7 weeks ago by
Erika
• 0 • written 8.7 years ago by
c.lieftink@nki.nl
▴ 30
5
votes
2
replies
1.2k
views
Is the VST implemented in DESeq useful on time-series cell differentiation datasets?
deseq
deseq2
vst
updated 6.4 years ago by
Wolfgang Huber
13k • written 6.4 years ago by
jiab
• 0
5
votes
3
replies
6.7k
views
What problem does the MA plot diagnose? And how do you solve it?
deseq2
deseq
rnaseq
updated 6.6 years ago by
Ryan C. Thompson
7.8k • written 6.6 years ago by
ysdel
▴ 40
5
votes
13
replies
5.1k
views
P values from Deseq Analysis
deseq
6.4 years ago
Shrikant Pawar
• 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
5.1 years ago
ansari.sarabio
• 0
4
votes
7
replies
3.0k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 5.0 years ago by
Michael Love
40k • written 5.0 years ago by
thindmarsmission
• 0
4
votes
6
replies
1.2k
views
DESeq2 design and stats question
deseq2
differential binding analysis
deseq
atac-seq
updated 5.7 years ago by
Michael Love
40k • written 5.7 years ago by
rbronste
▴ 60
4
votes
3
replies
2.4k
views
Why does Deseq, Deseq2, and EdgeR give vastly different results.
edger
deseq
deseq2
6.3 years ago
michael.steffen
▴ 20
4
votes
2
replies
7.4k
views
Analyzing RNA-Seq data without replicates using DESeq
deseq
DESeq2
updated 9.0 years ago by
Michael Love
40k • written 9.0 years ago by
solgakar@bi.technion.ac.il
▴ 90
4
votes
3
replies
3.2k
views
Add new columns to DESeqResults from text file by matching rownames.
deseq2
deseq
merge data frames
cbind
s4vectors
updated 6.0 years ago by
Michael Love
40k • written 6.0 years ago by
kirannbishwa01
• 0
4
votes
14
replies
15k
views
standard error value (lfcSE) returned by DeSeq2
deseq2
deseq
lfc
lfcse
standard error
updated 6.5 years ago by
rraadd_8
• 0 • written 6.5 years ago by
tootiki
• 0
4
votes
6
replies
1.3k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
24 months ago
s-rhussien
• 0
4
votes
4
replies
3.6k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.1 years ago by
wunderl
▴ 40 • written 4.2 years ago by
neekonsu
• 0
4
votes
7
replies
1.1k
views
Filtering DESeq2 result export along multiple lines
deseq2
differential binding analysis
deseq
updated 5.9 years ago by
Michael Love
40k • written 5.9 years ago by
rbronste
▴ 60
3
votes
4
replies
3.0k
views
Variance filtering prior to RNA-seq differential expression
sequencing
deseq
limma
updated 8.2 years ago by
Gordon Smyth
48k • written 8.2 years ago by
chris86
▴ 410
3
votes
7
replies
914
views
The discrepancy between the mean of extracted fitted value and calculated mean and SE based on LFC.
deseq2
deseq
5.1 years ago
blastzone.heimerdinger
▴ 10
3
votes
5
replies
6.7k
views
DESeq2 resultsNames output
deseq
deseq2
updated 8.6 years ago by
Michael Love
40k • written 8.6 years ago by
igor
▴ 40
3
votes
7
replies
1.9k
views
novice: building gene co-expression network using RNA-Seq data
rna-seq
WGCNA
deseq
method
coexpression
updated 5.4 years ago by
Peter Langfelder
★ 2.8k • written 5.4 years ago by
7kemZmani
▴ 10
3
votes
3
replies
1.8k
views
read counts of paired end reads for DESeq2 analysis
deseq
featurecounts
paired
updated 7.4 years ago by
Steve Lianoglou
13k • written 7.4 years ago by
tszn1984
• 0
3
votes
14
replies
17k
views
Normalization in DESeq2
deseq2
deseq
updated 8.8 years ago by
Michael Love
40k • written 8.8 years ago by
solgakar@bi.technion.ac.il
▴ 90
3
votes
4
replies
2.8k
views
DESeq is better than DESeq2?
deseq2
deseq
7.5 years ago
ribioinfo
▴ 100
3
votes
12
replies
1.2k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
4.6 years ago
ariel
▴ 10
3
votes
11
replies
3.0k
views
DESeq function taking too long
deseq2
deseq
factor
rnaseq
updated 6.2 years ago by
Peter Langfelder
★ 2.8k • written 6.2 years ago by
sup230
▴ 30
3
votes
1
reply
5.7k
views
Deseq for pairwise comparison among many pairs
DESeq
DESeq
updated 9.3 years ago by
Michael Love
40k • written 9.3 years ago by
Feng, Shihai
▴ 20
3
votes
8
replies
4.0k
views
DESeq / DESeq2 for translation efficiency in polysome profiling or ribsome profiling experiments
Sequencing
DESeq
Sequencing
DESeq
updated 7.1 years ago by
contactbiostructure
• 0 • written 9.8 years ago by
Guest User
★ 12k
3
votes
1
reply
1.1k
views
RNASeq testing for differential expression in one condition, equality in another (using DESeq)
deseq2
deseq
rnaseq
6.6 years ago
ysdel
▴ 40
3
votes
2
replies
11k
views
how to get normalized counts from edgeR
DESeq
DESeq
updated 11.2 years ago by
Mark Robinson
▴ 880 • written 11.2 years ago by
wang peter
★ 2.0k
3
votes
5
replies
2.1k
views
DESeq on transcripts v/s genes
DESeq
DESeq
updated 11.6 years ago by
Wolfgang Huber
13k • written 11.6 years ago by
Abhishek Pratap
▴ 410
3
votes
5
replies
2.5k
views
Using DESeq2: experimental design and extracting results
DESeq
DESeq2
DESeq
DESeq2
updated 9.3 years ago by
Michael Love
40k • written 9.3 years ago by
bio2001
▴ 60
3
votes
2
replies
2.7k
views
Nanostring ncounterdata - DESeq
RNASeq
Normalization
Preprocessing
DESeq
RNASeq
Normalization
Preprocessing
DESeq
updated 12.2 years ago by
Simon Anders
★ 3.7k • written 12.2 years ago by
Vanessa Vermeirssen
▴ 20
3
votes
5
replies
4.5k
views
Labeling points with hgnc symbols on the MA plot in DESeq2
deseq
MA
updated 7.2 years ago by
phil.chapman
▴ 150 • written 7.2 years ago by
spark27
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DMRcate design
by
Jitendra
▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block()
by
Koki
▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block
by
Koki
▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block
by
Hervé Pagès
16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block
by
Koki
▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Steps needed to change design (relevel factors) in DESeq2
Steps needed to change design (relevel factors) in DESeq2
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
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