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
241
views
evaluate the variable importance on genes
DESeq2
deseq
4 weeks ago
Meme
• 0
0
votes
2
replies
284
views
Running DESeq on normalized data
deseq
DESeq2
updated 3 months ago by
ATpoint
★ 4.0k • written 3 months ago by
Hugo
• 0
2
votes
2
replies
471
views
Predicting missing values splines DESeq2
deseq
DESeq2
4 months ago
georgii.vdovin
• 0
0
votes
1
reply
341
views
Controling for Covariates With a Continuous Predictor Variable
Deseq
DESeq2
updated 4 months ago by
Michael Love
41k • written 4 months ago by
georgii.vdovin
• 0
0
votes
1
reply
588
views
Can I transform already normalized rna-seq data with Z-score?
Z-score
RNASeqData
Deseq
DESeq2
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
khaserdene99
• 0
0
votes
3
replies
712
views
Difference between DESeqDataSetFromMatrix() function and DESeq() function
DESeq
DESeq2
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Abir.khazaal
▴ 10
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 7 months ago by
Erika
• 0 • written 9.2 years ago by
c.lieftink@nki.nl
▴ 40
0
votes
4
replies
568
views
lfc direction of effect flipped for ashr, apeGLM, but accurate to biological data for non-shrunken
DESeq2
apeglm
DESeq
ApeGLM
Ashr
updated 8 months ago by
Michael Love
41k • written 8 months ago by
Ndimensional
▴ 20
2
votes
5
replies
5.3k
views
ERROR configuration failed for package RCurl during installation of DESeq
ERROR: configuration failed for package ‘RCurl’
DESeq
written 4.0 years ago by
krunal.24.6
▴ 10
1
vote
2
replies
567
views
summarizeToGene in tximeta causing vastly different results
DESeq2
deseq
txime
tximeta
updated 11 months ago by
Michael Love
41k • written 11 months ago by
akrunic
• 0
0
votes
4
replies
1.1k
views
Volcano plot becomes flipped when I add a third condition
DESeq2
volcanoplot
deseq
HELP
contrast
updated 13 months ago by
Basti
▴ 750 • written 13 months ago by
Michael
• 0
0
votes
1
reply
532
views
What is the difference between these two arguments for log fold change shrinkage?
DESeq
updated 14 months ago by
Michael Love
41k • written 14 months ago by
m-bihie
▴ 10
0
votes
1
reply
662
views
Is it possible to convert transcript-level to gene-level dataset to use it in DESeq2 ?
DESeq2
Transcriptomics
tximport
deseq
txi
updated 14 months ago by
Dario Strbenac
★ 1.5k • written 14 months ago by
Hicham
▴ 10
0
votes
1
reply
2.7k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
graph
limma
convert
edgeR
DESeq
Rsubread
Normalization
graph
limma
convert
updated 15 months ago by
Gordon Smyth
50k • written 11.8 years ago by
Kasper Daniel Hansen
★ 6.5k
0
votes
2
replies
1.2k
views
suggestions/comments on DESeq transcript wise analysis
convert
DESeq
convert
DESeq
written 12.1 years ago by
Akula, Nirmala NIH/NIMH [C]
▴ 190
1
vote
1
reply
496
views
How to design multifactor DESEQ2 formula?
DESEQ
DESEQ2
updated 18 months ago by
ATpoint
★ 4.0k • written 18 months ago by
barrypraveen
• 0
3
votes
2
replies
879
views
DESeq2 is renaming gene names and lack of downregulated genes
DESeq
DESeq2
20 months ago
manwar
• 0
1
vote
1
reply
745
views
Gene wise dispersion estimate Process - From the prior to the posterior
GLM
prior
DESeq
LFC
updated 21 months ago by
Michael Love
41k • written 21 months ago by
stew
• 0
1
vote
5
replies
1.2k
views
Error in DEseq
DEseq
RNASeqData
updated 21 months ago by
ATpoint
★ 4.0k • written 21 months ago by
Sanatan
• 0
2
votes
1
reply
1.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 22 months ago by
swbarnes2
★ 1.3k • written 22 months ago by
Hicham
▴ 10
1
vote
5
replies
1.4k
views
Potential outlier/high variance
deseq
DESeq2
updated 23 months ago by
Michael Love
41k • written 23 months ago by
Amali Thrimawithana
• 0
1
vote
2
replies
858
views
Deseq2 with imbalanced design
Deseq
2.0 years ago
Alex
• 0
1
vote
4
replies
1.5k
views
Test if a gene is NOT differentially expressed in DESeq2?
DESeq2
deseq
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
penny.lane
• 0
0
votes
2
replies
1.0k
views
DESeqDataSet design issue
DESeq
DESeq2
2.3 years ago
matthew.valentine
• 0
19
votes
15
replies
58k
views
DESeq2 output explanation
deseq
deseq2
updated 2.4 years ago by
Michael Love
41k • written 9.4 years ago by
francesca.defilippis
▴ 100
9
votes
6
replies
9.9k
views
Error bars DESeq or DESeq2 fold change
rnaseq
deseq2
deseq
standard error
confidence interval
updated 2.4 years ago by
Michael Love
41k • written 8.0 years ago by
lisa.crossman
▴ 10
1
vote
1
reply
1.4k
views
DESeq2 rows did not converge in beta, how to solve
DESeq
DESeq2
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
n.vandis
• 0
4
votes
6
replies
1.6k
views
Interpretation of DESeq2 results with 3 factorial design with interaction terms.
r
DESeq
DESeq2
2.5 years ago
s-rhussien
• 0
2
votes
2
replies
2.2k
views
Correct way to make multiple comparisons on DESeq2?
DESeq
DESeq2
R
2.6 years ago • updated 2.5 years ago
jbnrodriguez
▴ 10
1
vote
2
replies
947
views
DESeq2 log2Foldchanges opposite sign for almost the same groups of comparison
RNASeq
DESeq
2.6 years ago
krawczyk.margarita
• 0
0
votes
2
replies
1.4k
views
same padj for all the genes after DEseq analysis
etLRT
WALD
edgeR
DESEq
updated 2.6 years ago by
Michael Love
41k • written 2.6 years ago by
aiswaryabioinfo
• 0
0
votes
1
reply
1.1k
views
Filtering DESeq2 results for | LFC | > 1 genes
RNAseq
LFC
DEseq
2.8 years ago
ayy2110
• 0
0
votes
7
replies
13k
views
Applying DESeq on RSEM output
edgeR
DESeq
edgeR
DESeq
updated 3.0 years ago by
mehdimerbah
• 0 • written 11.0 years ago by
dvir.tau@gmail.com
▴ 30
1
vote
2
replies
904
views
metage problem with DESeq
DESeq
metagene2
metagene
updated 3.0 years ago by
ericfournier2
▴ 10 • written 3.1 years ago by
GM
▴ 10
10
votes
14
replies
13k
views
how DESeq calculates p-value ?
deseq
differential gene expression
statistics
p-value
updated 3.1 years ago by
Kai_Qi
▴ 20 • written 8.1 years ago by
Giard
▴ 30
0
votes
3
replies
2.1k
views
Understanding MA plot distortion
DESeq2
MAplot
deseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
sp
• 0
0
votes
5
replies
1.6k
views
ZINB-WaVE-DESeq2 with Bulk Data: Choice of Epsilon value, K and gene number
DESeq2
ZINB
zinbwave
deseq
updated 3.1 years ago by
Michael Love
41k • written 3.1 years ago by
rowcyclecamp
• 0
2
votes
12
replies
4.4k
views
Deseq2: How to adjust for baseline read counts when testing for groups differences at post-treatment
deseq2
deseq
updated 3.4 years ago by
Michael Love
41k • written 8.9 years ago by
Nick
• 0
1
vote
2
replies
953
views
DESeq Error (nbinomTest ())
Deseq
nbinomTest
3.8 years ago
canfield
▴ 10
0
votes
7
replies
1.7k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
maniermk
• 0
2
votes
2
replies
823
views
Mocking data for understanding interactions in DESeq2
deseq2
deseq
updated 4.0 years ago by
Simon Anders
★ 3.7k • written 4.0 years ago by
blawney
• 0
3
votes
5
replies
2.0k
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 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
svlachavas
▴ 830
1
vote
9
replies
1.2k
views
Wrong results of DESeq compared to DESeq2 for some test cases?
deseq2
DESeq
updated 4.0 years ago by
Simon Anders
★ 3.7k • written 4.0 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
4.2 years ago
MANYA_BIOINFO
• 0
0
votes
1
reply
1.2k
views
DESeq2 counts function not working
deseq2
Deseq
RNAseq
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
mrfossl97
▴ 10
2
votes
3
replies
1.3k
views
DESeq2 2x2 factorial design: find genes unique to factor A?
deseq2
deseq
differential expression
contrasts
updated 4.4 years ago by
Michael Love
41k • written 4.4 years ago by
Keith Hughitt
▴ 180
4
votes
4
replies
4.4k
views
TMM Normalization: DESeqDataSet: some values in assay are negative
deseq2
deseq
normalization
updated 4.6 years ago by
wunderl
▴ 40 • written 4.7 years ago by
neekonsu
• 0
1
vote
2
replies
850
views
Filtering extraneous samples affects DESeq results. What is going on?
deseq
deseq2
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
sxv
• 0
0
votes
0
replies
909
views
Including sva results in SeqGSEA with data with batch effect
limma
deseq2
seqgsea
sva
deseq
4.7 years ago
kentfung
▴ 20
0
votes
9
replies
1.9k
views
NOOB question: How to use contrasts for subgroup analysis in DESeq2?
deseq
deseq2
contrast
subgroup
5.1 years ago
ariel
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
Answer: Microarray Limma Model fitting and DEG
Awards
• All
Popular Question
to
Pierre Lindenbaum
▴ 10
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Jenny Drnevich
★ 2.0k
Popular Question
to
Robert Castelo
★ 3.1k
Teacher
to
Peter Langfelder
★ 2.9k
Locations
• All
France,
just now
Italy,
3 minutes ago
India,
9 minutes ago
France,
10 minutes ago
Ghana,
11 minutes ago
Traffic: 732 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