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Showing :
DEseq
•
reset
2
votes
1
reply
62
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 4 days ago by
swbarnes2
★ 1.0k • written 5 days ago by
Hicham
• 0
1
vote
5
replies
233
views
Potential outlier/high variance
deseq
DESeq2
updated 25 days ago by
Michael Love
36k • written 5 weeks ago by
Amali Thrimawithana
• 0
1
vote
2
replies
127
views
Deseq2 with imbalanced design
Deseq
9 weeks ago
Alex
• 0
1
vote
4
replies
334
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 3 months ago by
Michael Love
36k • written 3 months ago by
penny.lane
• 0
0
votes
2
replies
240
views
DESeqDataSet design issue
DESeq
DESeq2
5 months ago
matthew.valentine
• 0
1
vote
1
reply
286
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 6 months ago by
Michael Love
36k • written 6 months ago by
n.vandis
• 0
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
2
votes
2
replies
580
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
8 months ago
jbnrodriguez
▴ 10
1
vote
2
replies
291
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
8 months ago
krawczyk.margarita
• 0
0
votes
2
replies
367
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 9 months ago by
Michael Love
36k • written 9 months ago by
aiswaryabioinfo
• 0
0
votes
1
reply
246
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
12 months ago
ayy2110
• 0
1
vote
2
replies
354
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 14 months ago by
ericfournier2
▴ 10 • written 14 months ago by
GM
▴ 10
0
votes
3
replies
585
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 14 months ago by
Michael Love
36k • written 14 months ago by
sp
• 0
0
votes
5
replies
653
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 15 months ago by
Michael Love
36k • written 15 months ago by
rowcyclecamp
• 0
1
vote
12
replies
2.8k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 18 months ago by
Michael Love
36k • written 7.0 years ago by
Nick
• 0
1
vote
2
replies
432
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
23 months ago
canfield
▴ 10
0
votes
7
replies
389
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 24 months ago by
Kevin Blighe
3.5k • written 24 months ago by
maniermk
• 0
2
votes
4
replies
985
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
updated 3 months ago by
Nicola
• 0 • written 2.1 years ago by
krunal.24.6
▴ 10
1
vote
2
replies
268
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 2.1 years ago by
Simon Anders
★ 3.7k • written 2.1 years ago by
blawney
• 0
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
1
vote
9
replies
492
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 2.2 years ago by
Simon Anders
★ 3.7k • written 2.2 years ago by
megapode32559
• 0
0
votes
7
replies
463
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2
deseq
2.3 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
498
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 2.5 years ago by
Michael Love
36k • written 2.5 years ago by
mrfossl97
▴ 10
2
votes
3
replies
597
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 2.5 years ago by
Michael Love
36k • written 2.5 years ago by
Keith Hughitt
▴ 150
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
1
vote
2
replies
410
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 2.8 years ago by
Michael Love
36k • written 2.8 years ago by
sxv
• 0
0
votes
0
replies
471
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
2.9 years ago
kentfung
• 0
0
votes
9
replies
828
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
3.2 years ago
ariel
▴ 10
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
2
votes
3
replies
1000
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 3.5 years ago by
Michael Love
36k • written 3.5 years ago by
lefeverde
▴ 10
0
votes
1
reply
471
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 3.5 years ago by
Michael Love
36k • written 3.5 years ago by
FaisalH
• 0
0
votes
3
replies
607
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2
rnaseq
rna-seq
deseq2
deseq
3.6 years ago
Ben
▴ 50
0
votes
7
replies
2.9k
views
DESeq2 install problem
deseq
updated 3.6 years ago by
Michael Love
36k • written 3.6 years ago by
bikashten
• 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
0
votes
3
replies
544
views
DESeq2 group comparison
deseq2
deseq
differential binding analysis
updated 3.7 years ago by
Michael Love
36k • written 3.7 years ago by
rbronste
▴ 60
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
0
votes
7
replies
663
views
Deseq 2 multiple comparisons (3 groups, 24 samples)
deseq
updated 3.7 years ago by
Michael Love
36k • written 3.7 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
3.7 years ago
ansari.sarabio
• 0
1
vote
5
replies
561
views
Group Specific Condition Query
deseq2
deseq
batcheffect
updated 3.8 years ago by
Michael Love
36k • written 3.8 years ago by
bdy8
• 0
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
0
votes
8
replies
1.1k
views
DESeq2 Multi factor, multi time point comparison design formula
rna-seq
deseq2
deseq
R
updated 3.8 years ago by
Michael Love
36k • written 3.8 years ago by
arun.thirumaran
• 0
0
votes
1
reply
434
views
how to start normalization
deseq
3.8 years ago
raghavaraghava049
• 0
0
votes
1
reply
498
views
Basemean always multiples of 0.5 in deseq2 results
deseq
results
baseMean
updated 3.8 years ago by
Michael Love
36k • written 3.9 years ago by
batmaiden
• 0
0
votes
3
replies
482
views
3x2 comparisons in DEseq - time (3 time points) and two treatments
deseq2
deseq
rna-seq
multiple comparisons
updated 3.9 years ago by
Michael Love
36k • written 3.9 years ago by
rbronste
▴ 60
2
votes
3
replies
842
views
ASE using DESeq2
deseq2
deseq
normalization
allele specific expression
rnaseq
updated 4.0 years ago by
Simon Anders
★ 3.7k • written 4.0 years ago by
c.martinezruiz
• 0
0
votes
5
replies
696
views
How to simulate time course RNA seq data using DESeq?
deseq2
R
makeexampledeseqdataset
deseq
updated 4.0 years ago by
Michael Love
36k • written 4.0 years ago by
kjkjindal
• 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
1
vote
2
replies
870
views
Deseq2 with replicate mean and variance information
deseq2
deseq
differential analysis
proteomics
4.1 years ago
blehtine
• 0
1
vote
8
replies
1.5k
views
DESeq2 : group specific effect of a treatment while controlling for individual effect
deseq2
DESeq
design and contrast matrix
deseq
4.2 years ago
SPbeginner
• 0
1
vote
3
replies
712
views
DEseq2 sample imbalance
deseq
4.2 years ago
aishu.jp
▴ 20
50 results • Page
1 of 1
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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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