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DEseq
•
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0
votes
1
reply
41
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 1 day ago by
ATpoint
★ 2.1k • written 1 day ago by
m-bihie
• 0
0
votes
1
reply
105
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 10 days ago by
Dario Strbenac
★ 1.5k • written 11 days ago by
Hicham
• 0
0
votes
2
replies
759
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 11.0 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
173
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 4 months ago by
ATpoint
★ 2.1k • written 4 months ago by
barrypraveen
• 0
3
votes
2
replies
286
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
6 months ago
manwar
• 0
1
vote
1
reply
278
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 7 months ago by
Michael Love
39k • written 7 months ago by
stew
• 0
1
vote
5
replies
405
views
Error in DEseq
DEseq
RNASeqData
updated 7 months ago by
ATpoint
★ 2.1k • written 7 months ago by
Sanatan
• 0
2
votes
1
reply
444
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 8 months ago by
swbarnes2
★ 1.2k • written 8 months ago by
Hicham
• 0
1
vote
5
replies
584
views
Potential outlier/high variance
deseq
DESeq2
updated 9 months ago by
Michael Love
39k • written 9 months ago by
Amali Thrimawithana
• 0
1
vote
2
replies
330
views
Deseq2 with imbalanced design
Deseq
10 months ago
Alex
• 0
1
vote
4
replies
659
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 12 months ago by
Michael Love
39k • written 12 months ago by
penny.lane
• 0
0
votes
2
replies
479
views
DESeqDataSet design issue
DESeq
DESeq2
13 months ago
matthew.valentine
• 0
1
vote
1
reply
591
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 15 months ago by
Michael Love
39k • written 15 months ago by
n.vandis
• 0
4
votes
6
replies
858
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
16 months ago
s-rhussien
• 0
2
votes
2
replies
1.1k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
17 months ago • updated 16 months ago
jbnrodriguez
▴ 10
1
vote
2
replies
448
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
17 months ago
krawczyk.margarita
• 0
0
votes
2
replies
671
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 17 months ago by
Michael Love
39k • written 17 months ago by
aiswaryabioinfo
• 0
0
votes
1
reply
480
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
20 months ago
ayy2110
• 0
1
vote
2
replies
534
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 22 months ago by
ericfournier2
▴ 10 • written 23 months ago by
GM
▴ 10
0
votes
3
replies
1.1k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 23 months ago by
Michael Love
39k • written 23 months ago by
sp
• 0
0
votes
5
replies
951
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 24 months ago by
Michael Love
39k • written 24 months ago by
rowcyclecamp
• 0
2
votes
12
replies
3.2k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 2.2 years ago by
Michael Love
39k • written 7.7 years ago by
Nick
• 0
1
vote
2
replies
572
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
2.6 years ago
canfield
▴ 10
0
votes
7
replies
730
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 2.7 years ago by
Kevin Blighe
3.7k • written 2.7 years ago by
maniermk
• 0
2
votes
4
replies
2.4k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
updated 11 months ago by
Nicola
• 0 • written 2.8 years ago by
krunal.24.6
▴ 10
1
vote
2
replies
376
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 2.8 years ago by
Simon Anders
★ 3.7k • written 2.8 years ago by
blawney
• 0
3
votes
5
replies
1.0k
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 2.8 years ago by
Michael Love
39k • written 2.8 years ago by
svlachavas
▴ 800
1
vote
9
replies
659
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 2.9 years ago by
Simon Anders
★ 3.7k • written 2.9 years ago by
megapode32559
• 0
0
votes
7
replies
584
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2
deseq
3.0 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
679
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 3.1 years ago by
Michael Love
39k • written 3.1 years ago by
mrfossl97
▴ 10
2
votes
3
replies
807
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 3.2 years ago by
Michael Love
39k • written 3.2 years ago by
Keith Hughitt
▴ 180
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
1
vote
2
replies
515
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 3.5 years ago by
Michael Love
39k • written 3.5 years ago by
sxv
• 0
0
votes
0
replies
596
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
3.6 years ago
kentfung
▴ 10
0
votes
9
replies
1.1k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
3.9 years ago
ariel
▴ 10
3
votes
12
replies
912
views
Why did I get NA p-values in DESeq with continuous variable?
deseq2
p-value
continuous
deseq
3.9 years ago
ariel
▴ 10
2
votes
3
replies
1.2k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 4.1 years ago by
Michael Love
39k • written 4.1 years ago by
lefeverde
▴ 10
0
votes
1
reply
595
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 4.2 years ago by
Michael Love
39k • written 4.2 years ago by
FaisalH
• 0
0
votes
3
replies
729
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2
rnaseq
rna-seq
deseq2
deseq
4.3 years ago
Ben
▴ 50
0
votes
7
replies
3.3k
views
DESeq2 install problem
deseq
updated 4.3 years ago by
Michael Love
39k • written 4.3 years ago by
bikashten
• 0
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
0
votes
3
replies
658
views
DESeq2 group comparison
deseq2
deseq
differential binding analysis
updated 4.3 years ago by
Michael Love
39k • written 4.3 years ago by
rbronste
▴ 60
3
votes
5
replies
725
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
0
votes
7
replies
774
views
Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
Matthew.baldwin
• 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
4.4 years ago
ansari.sarabio
• 0
1
vote
5
replies
696
views
Group Specific Condition Query
deseq2
deseq
batcheffect
updated 4.4 years ago by
Michael Love
39k • written 4.4 years ago by
bdy8
• 0
3
votes
7
replies
710
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
0
votes
8
replies
1.4k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq
deseq2
deseq
R
updated 4.5 years ago by
Michael Love
39k • written 4.5 years ago by
arun.thirumaran
• 0
0
votes
1
reply
512
views
how to start normalization
deseq
4.5 years ago
raghavaraghava049
• 0
0
votes
1
reply
611
views
Basemean always multiples of 0.5 in deseq2 results
deseq
results
baseMean
updated 4.5 years ago by
Michael Love
39k • written 4.5 years ago by
batmaiden
• 0
50 results • Page
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Replies
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I felt that my way of analyzing this data set was a bit unfortunate. I was not involved in the experimental design myself and am now trying…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
For tissue T1 and each time point, each replicate corresponds to a single plant. For tissue T2, we actually had to sample 5 plants per rep…
Answer: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
> Due to the high degree of heterozygosity of the plants used for the experiment, we thought it best to pool the same tissue under the same…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
How many plants are used for each of the biological replicate samples? One plant or a few?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
Yes you are right, we have 24 RNA-seq libraries in total. The replicates come from the same population of plants, but independent from tho…
Votes
DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
A: DESeq2 pairwise comparisons w/ 3 factors
Comment: MA plot
Comment: MA plot
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