Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
DEseq
•
reset
1
vote
2
replies
316
views
evaluate the variable importance on genes
DESeq2
deseq
10 weeks ago
Meme
• 0
0
votes
2
replies
337
views
Running DESeq on normalized data
deseq
DESeq2
updated 4 months ago by
ATpoint
★ 4.1k • written 4 months ago by
Hugo
• 0
2
votes
2
replies
523
views
Predicting missing values splines DESeq2
deseq
DESeq2
5 months ago
georgii.vdovin
• 0
0
votes
1
reply
382
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 5 months ago by
Michael Love
41k • written 5 months ago by
georgii.vdovin
• 0
0
votes
1
reply
654
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
khaserdene99
• 0
0
votes
3
replies
891
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
Abir.khazaal
▴ 10
0
votes
4
replies
657
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Ndimensional
▴ 20
1
vote
2
replies
611
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 12 months ago by
Michael Love
41k • written 12 months ago by
akrunic
• 0
0
votes
4
replies
1.2k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 14 months ago by
Basti
▴ 780 • written 14 months ago by
Michael
• 0
0
votes
1
reply
566
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 15 months ago by
Michael Love
41k • written 15 months ago by
m-bihie
▴ 10
0
votes
1
reply
728
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 15 months ago by
Dario Strbenac
★ 1.5k • written 15 months ago by
Hicham
▴ 10
0
votes
2
replies
1.2k
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 12.2 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
520
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 20 months ago by
ATpoint
★ 4.1k • written 20 months ago by
barrypraveen
• 0
3
votes
2
replies
926
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
21 months ago
manwar
• 0
1
vote
1
reply
780
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 22 months ago by
Michael Love
41k • written 23 months ago by
stew
• 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq
RNASeqData
updated 23 months ago by
ATpoint
★ 4.1k • written 23 months ago by
Sanatan
• 0
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 23 months ago by
swbarnes2
★ 1.3k • written 23 months ago by
Hicham
▴ 10
1
vote
5
replies
1.4k
views
Potential outlier/high variance
deseq
DESeq2
updated 2.0 years ago by
Michael Love
41k • written 2.1 years ago by
Amali Thrimawithana
• 0
1
vote
2
replies
916
views
Deseq2 with imbalanced design
Deseq
2.1 years ago
Alex
• 0
1
vote
4
replies
1.6k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 2.3 years ago by
Michael Love
41k • written 2.3 years ago by
penny.lane
• 0
0
votes
2
replies
1.1k
views
DESeqDataSet design issue
DESeq
DESeq2
2.4 years ago
matthew.valentine
• 0
1
vote
1
reply
1.5k
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
n.vandis
• 0
4
votes
6
replies
1.7k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
2.6 years ago
s-rhussien
• 0
2
votes
2
replies
2.3k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
2.7 years ago • updated 2.6 years ago
jbnrodriguez
▴ 10
1
vote
2
replies
985
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
2.7 years ago
krawczyk.margarita
• 0
0
votes
2
replies
1.5k
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
aiswaryabioinfo
• 0
0
votes
1
reply
1.1k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
2.9 years ago
ayy2110
• 0
1
vote
2
replies
940
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 3.1 years ago by
ericfournier2
▴ 10 • written 3.2 years ago by
GM
▴ 10
0
votes
3
replies
2.2k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
sp
• 0
0
votes
5
replies
1.7k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 3.2 years ago by
Michael Love
41k • written 3.2 years ago by
rowcyclecamp
• 0
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
41k • written 9.0 years ago by
Nick
• 0
1
vote
2
replies
982
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
3.9 years ago
canfield
▴ 10
0
votes
7
replies
1.8k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
maniermk
• 0
2
votes
5
replies
5.6k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
written 4.1 years ago by
krunal.24.6
▴ 10
2
votes
2
replies
865
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 4.1 years ago by
Simon Anders
★ 3.7k • written 4.1 years ago by
blawney
• 0
3
votes
5
replies
2.1k
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 4.1 years ago by
Michael Love
41k • written 4.1 years ago by
svlachavas
▴ 830
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
0
votes
7
replies
1.1k
views
how to analyze and find differentially expressed genes based on miRNA gene raw read counts?
deseq2
deseq
4.3 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
1.2k
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
mrfossl97
▴ 10
2
votes
3
replies
1.4k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.5 years ago by
Michael Love
41k • written 4.5 years ago by
Keith Hughitt
▴ 180
4
votes
4
replies
4.5k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.7 years ago by
wunderl
▴ 40 • written 4.8 years ago by
neekonsu
• 0
1
vote
2
replies
891
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
sxv
• 0
0
votes
0
replies
944
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
4.8 years ago
kentfung
▴ 20
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
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
2
votes
3
replies
1.9k
views
DESeq2 count outlier replacement from Cook's threshold
deseq2
deseq
rnaseq
outliers
count outliers
updated 5.4 years ago by
Michael Love
41k • written 5.4 years ago by
lefeverde
▴ 10
0
votes
1
reply
1.0k
views
Question about multi-factor Deseq analysis
DESeq
deseq2
microbiome
gut microbiome
updated 5.5 years ago by
Michael Love
41k • written 5.5 years ago by
FaisalH
• 0
0
votes
3
replies
1.2k
views
Strange lfcShrink plot when running DESeq2 workflow
DESeq2
rnaseq
rna-seq
deseq2
deseq
5.6 years ago
Ben
▴ 50
0
votes
7
replies
3.9k
views
DESeq2 install problem
deseq
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
bikashten
• 0
5
votes
7
replies
3.6k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
thindmarsmission
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards
• All
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Zainab
• 0
Popular Question
to
Theo
▴ 10
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Locations
• All
France,
21 minutes ago
Sweden,
32 minutes ago
WEHI, Melbourne, Australia,
1 hour ago
Miami, FL,
2 hours ago
Sweden,
2 hours ago
Traffic: 472 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6