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
0
votes
0
replies
3
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
20 minutes ago
gene_bioconductor
▴ 10
0
votes
0
replies
7
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
1 hour ago
z_bahari
• 0
0
votes
0
replies
9
views
Gene-by-sample covariates in limma
Metabolomics
limma
1 hour ago
c53aba27
• 0
0
votes
0
replies
8
views
flowStats for CyTOF
flowStats
2 hours ago
tholmes
• 0
0
votes
2
replies
32
views
DESeq2 v1.35.0
DESeq2
updated 3 hours ago by
Michael Love
41k • written 3 hours ago by
Espresso
• 0
5
votes
6
replies
2.7k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 2 hours ago by
James W. MacDonald
65k • written 2.3 years ago by
yanchangjian2019
• 0
0
votes
0
replies
13
views
DiffBind: no peaks in DBA object
DiffBind
macs2
chipseq
4 hours ago
yvonneh
• 0
0
votes
0
replies
12
views
How to create consensus peak sets for each group to use in DiffBind?
DiffBind
4 hours ago
Ian D.
▴ 70
0
votes
2
replies
81
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
1 day ago • updated 4 hours ago
Ian D.
▴ 70
0
votes
1
reply
26
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
JobPosting
written 9 hours ago by
4r-rtg
• 0
0
votes
3
replies
89
views
Differences in differential analysis methods for RNA-Seq
DESeq2
StatisticalMethod
Proteomics
DifferentialExpression
RNASeq
updated 9 hours ago by
ATpoint
★ 4.1k • written 21 hours ago by
james.zhang20
• 0
0
votes
1
reply
47
views
Deseq2 and Normalization of RNA sequencing data
DESeq2
updated 10 hours ago by
ATpoint
★ 4.1k • written 20 hours ago by
kcarey
• 0
0
votes
2
replies
149
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 9 days ago by
taur.vil
• 0
0
votes
2
replies
187
views
Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation
SequenceAnnotation
MethylationArray
GenomicDistributionsData
1 day ago • updated 18 hours ago
Yveto
• 0
0
votes
3
replies
213
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 22 hours ago by
Michael Love
41k • written 1 day ago by
HAK
• 0
0
votes
0
replies
54
views
Empty table plot using plotGseaTable()
fgsea
1 day ago • updated 22 hours ago
Chris
• 0
0
votes
1
reply
93
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 23 hours ago by
ATpoint
★ 4.1k • written 23 hours ago by
angelathuynh5
• 0
3
votes
0
replies
39
views
News:
Bioconductor 3.19 is Released!
Release
Bioconductor
Packages
Software
23 hours ago
shepherl
3.9k
14
votes
17
replies
1.1k
views
Why p value inconsistent when using different number of pathway score?
limma
12 days ago • updated 1 day ago
Chris
• 0
0
votes
3
replies
106
views
Store output of matchPWM()
biostrings
Biostrings
updated 1 day ago by
James W. MacDonald
65k • written 1 day ago by
mat149
▴ 70
1
vote
4
replies
452
views
DEseq2 coefficient
DESeq2
coefficient
9 weeks ago • updated 1 day ago
JKim
• 0
8
votes
6
replies
1.7k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq
rnaseq
updated 1 day ago by
Leonard Goldstein
▴ 200 • written 6.7 years ago by
Sylvain Foisy
▴ 80
3
votes
4
replies
165
views
Help with error using camera() in limma
CAMERA
limma
2 days ago
Chris
• 0
2
votes
2
replies
1.0k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 2 days ago by
XW
• 0 • written 7.9 years ago by
tati6406
• 0
0
votes
3
replies
1.5k
views
Limma, eBayes different sample size of groups and adjustment
limma
limma
updated 2 days ago by
XW
• 0 • written 13.0 years ago by
Babara Mueller
▴ 10
0
votes
1
reply
203
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
SSSJec
• 0
0
votes
3
replies
204
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery
ArrayExpress
limma
DifferentialExpression
updated 2 days ago by
James W. MacDonald
65k • written 3 days ago by
SSSJec
• 0
15
votes
23
replies
1.9k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
4 weeks ago • updated 2 days ago
Chris
• 0
6
votes
19
replies
2.4k
views
DESeq2 a lot of genes showing up as differentially expressed that only have 1 sample with any expression
deseq2
updated 2 days ago by
Sey R.
• 0 • written 4.6 years ago by
hsbio
▴ 10
0
votes
3
replies
154
views
Different number of exons in reference genome affects DEXSeq analysis
DEXSeq
updated 2 days ago by
Alejandro Reyes
★ 1.9k • written 14 days ago by
Alessia
• 0
1
vote
1
reply
78
views
Fold change calculation in Diffbind vs. DESEQ2?
DiffBind
ChIPSeqData
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
marcusn
• 0
0
votes
1
reply
74
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Aurora
• 0
0
votes
1
reply
85
views
Padj "NA" with thousands of low count although the raw read counts are quite large
DESeq2
updated 2 days ago by
Michael Love
41k • written 2 days ago by
Agung
• 0
0
votes
0
replies
44
views
News:
BioC2024 deadlines approaching
BioC2024
Bioconductor
Community
2 days ago
Maria Doyle
▴ 70
0
votes
1
reply
59
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 2 days ago by
shepherl
3.9k • written 2 days ago by
bounlu
• 0
0
votes
1
reply
82
views
putting my own expression data in deseq2
DESeq2
updated 2 days ago by
ATpoint
★ 4.1k • written 2 days ago by
Dev
• 0
2
votes
2
replies
167
views
Perform gene set enrichment analysis using fgsea on two conditions that don't have differential express genes
fgsea
3 days ago • updated 2 days ago
Chris
• 0
0
votes
0
replies
54
views
Could we detect difference at pathway level but not significant different at gene level?
GSVA
3 days ago
Chris
• 0
0
votes
4
replies
237
views
Minfi - estimatecellscount
min
minfi
updated 3 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
3
votes
3
replies
195
views
DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
DESeq2
contrasts
updated 3 days ago by
ATpoint
★ 4.1k • written 3 days ago by
bioinf
▴ 10
0
votes
0
replies
70
views
how to do Differential splicing from SGSeq analysis
DEXSeq
SGSeq
8 days ago • updated 3 days ago
Sara
• 0
1
vote
1
reply
106
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 5 days ago by
Leo Lahti
▴ 40 • written 6 days ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
293
views
Math expression in shapeCustom legend in EnhancedVolcano
EnhancedVolcano
7 days ago • updated 6 days ago
pl23
• 0
0
votes
2
replies
181
views
PCA plot suggestions
DESeq2
PCAtools
updated 6 days ago by
Michael Love
41k • written 7 days ago by
Aaliya
• 0
1
vote
2
replies
694
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
15 days ago • updated 6 days ago
ussarizona
▴ 10
1
vote
3
replies
186
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 6 days ago by
Michael Love
41k • written 6 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
113
views
ATACseq merge peaks
DiffBind
updated 6 days ago by
ATpoint
★ 4.1k • written 8 days ago by
Shloka
• 0
1
vote
1
reply
150
views
Improving the design matrices vignette in RNAseq123
RNAseq123
updated 6 days ago by
Gordon Smyth
50k • written 10 days ago by
Lluís Revilla Sancho
▴ 730
1
vote
4
replies
299
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
8 days ago • updated 6 days ago
winwater0928
• 0
2
votes
9
replies
341
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 6 days ago by
James W. MacDonald
65k • written 7 days ago by
Alexandre
• 0
206 results • Page
1 of 5
Recent ...
Replies
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
James W. MacDonald
65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Answer: DESeq2 v1.35.0
by
James W. MacDonald
65k
Odd release versions indicate a devel version, which upon release is incremented to the next even version, so you won't be able to find tha…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
fatinataly
• 0
I tried also with oligo does not work, any other suggestion?
Comment: More regions in union when increasing DBA$config$mergeOverlap
by
Ian D.
▴ 70
Hello. Thanks for the reply. Sorry about this. My testing is telling me that 1 is the default (a gap), not -1 (1bp overlap). Negative …
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
Awards
• All
Popular Question
to
gene_bioconductor
▴ 10
Popular Question
to
rohitsatyam102
▴ 20
Popular Question
to
shepherl
3.9k
Popular Question
to
siajunren
• 0
Scholar
to
Rory Stark
★ 5.2k
Locations
• All
France,
4 minutes ago
United States,
15 minutes ago
European Union,
18 minutes ago
United States,
18 minutes ago
EMBL Heidelberg,
23 minutes ago
Traffic: 789 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