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deseq
•
reset
41
votes
44
replies
10k
views
Are published RNA seq data analyses often wrong in calculating p-values and FDR?
FDR
p-value
DESeq
RNA-Seq
updated 6.4 years ago by
Wade Davis
▴ 60 • written 7.0 years ago by
yjiangnan
▴ 10
0
votes
31
replies
4.3k
views
Error in find DEXSeq package
deseq
dexseq
9.0 years ago
engr.yahya602
• 0
26
votes
22
replies
19k
views
DESeq2 for ChIP-seq differential peaks
deseq2
deseq
chipseq
updated 6.8 years ago by
k.vitting.seerup
▴ 120 • written 8.7 years ago by
tangming2005
▴ 190
2
votes
19
replies
2.9k
views
phyloseq/DESeq gives negative transformed values
Microbiome
DESeq
Microbiome
DESeq
updated 10.0 years ago by
Michael Love
42k • written 10.1 years ago by
Sophie Josephine Weiss
▴ 130
7
votes
18
replies
8.3k
views
Differential expression analysis: Continuous variables
DESeq
EdgeR
limma
8.6 years ago
Radek
▴ 90
9
votes
17
replies
1.8k
views
DESeq2 design subcategories
deseq2
deseq
differential binding analysis
updated 6.4 years ago by
Michael Love
42k • written 6.4 years ago by
rbronste
▴ 60
0
votes
17
replies
2.4k
views
Low number of replicates DESeq
Normalization
DESeq
Normalization
DESeq
updated 10.2 years ago by
Steve Lianoglou
★ 13k • written 10.2 years ago by
Federico Gaiti
▴ 130
0
votes
17
replies
2.7k
views
[Bioc] RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing
RNASeq
Microarray
qPCR
Coverage
edgeR
DESeq
Sequencing
RNASeq
Microarray
qPCR
updated 11.0 years ago by
Steve Lianoglou
★ 13k • written 11.0 years ago by
Lucia Peixoto
▴ 330
1
vote
17
replies
5.6k
views
Filtering out tags with low counts in DESeq and EgdeR?
Normalization
edgeR
DESeq
Normalization
edgeR
DESeq
13.0 years ago
Xiaohui Wu
▴ 280
1
vote
15
replies
3.9k
views
DEseq for chip-seq data normalisation
DESeq
DESeq2
DESeq
DESeq2
updated 10.5 years ago by
Ying W
▴ 90 • written 10.5 years ago by
Giuseppe Gallone
▴ 170
19
votes
15
replies
59k
views
DESeq2 output explanation
deseq
deseq2
updated 2.5 years ago by
Michael Love
42k • written 9.5 years ago by
francesca.defilippis
▴ 100
10
votes
14
replies
4.3k
views
Why limma, edgeR, and DESeq did not implement fold change moderation first?
limma
edger
deseq
deseq2
updated 6.6 years ago by
Gordon Smyth
50k • written 6.6 years ago by
Nik Tuzov
▴ 80
3
votes
14
replies
18k
views
Normalization in DESeq2
deseq2
deseq
updated 9.4 years ago by
Michael Love
42k • written 9.4 years ago by
solgakar@bi.technion.ac.il
▴ 90
4
votes
14
replies
17k
views
standard error value (lfcSE) returned by DeSeq2
deseq2
deseq
lfc
lfcse
standard error
updated 7.1 years ago by
rraadd_8
• 0 • written 7.2 years ago by
tootiki
• 0
1
vote
14
replies
10k
views
DESeq Error in round(assay(se)) : non-numeric argument to mathematical function
deseq
rna-seq
9.1 years ago
rodriguez.varenka
• 0
0
votes
14
replies
2.4k
views
(no subject)
DESeq
DESeq
updated 11.1 years ago by
Deisy Gysi
▴ 20 • written 11.2 years ago by
Liu, XiaoChuan
▴ 30
10
votes
14
replies
13k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 3.2 years ago by
Kai_Qi
▴ 20 • written 8.2 years ago by
Giard
▴ 30
0
votes
13
replies
3.3k
views
DESeq and number of replicates required for RNA-Seq
GO
DESeq
GO
DESeq
updated 13.9 years ago by
Naomi Altman
★ 6.0k • written 13.9 years ago by
michael watson IAH-C
★ 3.4k
1
vote
13
replies
5.3k
views
'Codetools' and 'mgcv' packages fail to update
package updates
codetools
deseq
mgcv
updated 9.1 years ago by
rodrigo_sengo
• 0 • written 9.1 years ago by
pbhamidipati
• 0
5
votes
13
replies
5.8k
views
P values from Deseq Analysis
deseq
7.0 years ago
Shrikant Pawar
• 0
0
votes
13
replies
6.6k
views
Up & Downregulated genes using DESeq
DESeq
DESeq
updated 12.1 years ago by
Sunny Yu Liu
▴ 80 • written 12.1 years ago by
OD
▴ 40
3
votes
12
replies
1.6k
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
5.2 years ago
ariel
▴ 20
7
votes
12
replies
9.0k
views
Confused in the usage of formula in DESeq or DESeq2
deseq2
deseq
updated 6.9 years ago by
bio2001
▴ 60 • written 9.5 years ago by
skyoflcz
▴ 20
0
votes
12
replies
2.4k
views
problem with loading DESeq after upgrading from R 2.14 to R 2.15
GUI
DESeq
DEXSeq
GUI
DESeq
DEXSeq
updated 12.0 years ago by
Yue Li
▴ 60 • written 12.0 years ago by
Yue Li
▴ 370
2
votes
12
replies
4.5k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 3.5 years ago by
Michael Love
42k • written 9.0 years ago by
Nick
• 0
0
votes
12
replies
3.0k
views
DEseq version and R version compatibility
DESeq
DESeq
updated 11.6 years ago by
Thomas Girke
★ 1.7k • written 11.6 years ago by
José Luis Lavín
▴ 280
6
votes
12
replies
17k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2
deseq
counts
rnaseq
differential gene expression
updated 8.0 years ago by
Michael Love
42k • written 8.0 years ago by
wannes.nauwynck
▴ 10
25
votes
11
replies
7.8k
views
Normalization methodology in DESeq/DESeq2 vs edgeR
deseq
deseq2
edgeR
normalization
updated 8.5 years ago by
Simon Anders
★ 3.7k • written 8.5 years ago by
Nik Tuzov
▴ 80
3
votes
11
replies
3.5k
views
DESeq function taking too long
deseq2
deseq
factor
rnaseq
updated 6.8 years ago by
Peter Langfelder
★ 3.0k • written 6.8 years ago by
sup230
▴ 30
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 9 months ago by
Erika
• 0 • written 9.3 years ago by
c.lieftink@nki.nl
▴ 40
0
votes
10
replies
4.3k
views
DESeq2, error: inv(): matrix appears to be singular
deseq
9.6 years ago
sandramg82
• 0
0
votes
10
replies
2.1k
views
Multifactor analysis with deseq
Normalization
DESeq
DESeq2
Normalization
DESeq
DESeq2
updated 11.1 years ago by
Simon Anders
★ 3.7k • written 11.1 years ago by
Michael Muratet
▴ 420
0
votes
10
replies
2.4k
views
DESeq /edgeR design problem for a small RNASeq
RNASeq
edgeR
DESeq
RNASeq
edgeR
DESeq
updated 10.9 years ago by
Gordon Smyth
50k • written 10.9 years ago by
Eduardo Andrés León
▴ 90
0
votes
10
replies
1.5k
views
re incomplete analysis in Deseq
DESeq
DESeq
updated 12.2 years ago by
Wolfgang Huber
★ 13k • written 12.2 years ago by
Guest User
★ 13k
2
votes
10
replies
3.3k
views
DESeq2 results export padj sorted
deseq2
deseq
differential binding analysis
updated 6.3 years ago by
Michael Love
42k • written 6.3 years ago by
rbronste
▴ 60
0
votes
10
replies
1.5k
views
DESeq on CCAT identified chipseq peaks
ChIPSeq
chipseq
DESeq
ChIPSeq
chipseq
DESeq
updated 10.0 years ago by
Rory Stark
★ 5.2k • written 10.0 years ago by
Guest User
★ 13k
2
votes
10
replies
5.1k
views
DESEQ2 with 3 biological replicates for control and 1 biological replicate for treatment
DESEQ
deseq2
deseq
replicates
biologicalreplicates
8.4 years ago
wd
▴ 30
0
votes
10
replies
2.0k
views
What is the effect of setting modelMatrixType="standard"
deseq2
modelMatrixType
DESeq
updated 8.4 years ago by
Michael Love
42k • written 8.4 years ago by
Gregory Warnes
▴ 50
1
vote
9
replies
1.3k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 4.1 years ago by
Simon Anders
★ 3.7k • written 4.1 years ago by
megapode32559
• 0
2
votes
9
replies
7.5k
views
Multiple alignments (multi-mapped reads) and DESeq/edgeR pipeline
deseq
deseq2
edger
tophat
bowtie
8.9 years ago
ysdel
▴ 40
0
votes
9
replies
4.7k
views
DESeq2 unequal sample sizes
deseq2
deseq
sample size
6.6 years ago
MrHodor
• 0
0
votes
9
replies
2.0k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.2 years ago
ariel
▴ 20
0
votes
9
replies
1.6k
views
How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis
Normalization
DESeq
Normalization
DESeq
updated 12.0 years ago by
Wolfgang Huber
★ 13k • written 12.0 years ago by
Marie Sémon
▴ 50
0
votes
9
replies
2.4k
views
Recommended gene model for DESeq
DESeq
DESeq
updated 12.1 years ago by
Simon Anders
★ 3.7k • written 12.1 years ago by
Assaf Gordon
▴ 30
0
votes
9
replies
1.8k
views
deseq for multiple groups with no replicate
DESeq
DESeq
updated 13.1 years ago by
Wolfgang Huber
★ 13k • written 13.1 years ago by
Yolande Tra
▴ 120
0
votes
9
replies
3.8k
views
DESeq vs DESeq2 have different DEGs results
DESeq
DESeq2
DESeq
DESeq2
10.0 years ago
Catalina Aguilar Hurtado
▴ 90
14
votes
9
replies
15k
views
How does DESeq2 handle zero counts in one condition?
deseq2
deseq
rna-seq
9.3 years ago
gavrielmatt
▴ 30
15
votes
8
replies
11k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2
deseq
9.5 years ago
salahm
▴ 70
0
votes
8
replies
2.0k
views
Experimental design for RNA-Seq
edgeR
DEGseq
DESeq
edgeR
DEGseq
DESeq
updated 14.0 years ago by
Naomi Altman
★ 6.0k • written 14.0 years ago by
michael watson IAH-C
★ 3.4k
0
votes
8
replies
1.9k
views
Fwd: differential binding question
edgeR
DESeq
edgeR
DESeq
updated 12.3 years ago by
Rory Stark
▴ 100 • written 12.3 years ago by
mali salmon
▴ 370
50 results • Page
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Many thanks and it also resolved the same issue for me!
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I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
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