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
7
replies
370
views
Methylation Analysis experiment design using Limma
DNAMethylation
limma
methylationArrayAnalysis
4 weeks ago • updated 28 days ago
hortense96
• 0
0
votes
2
replies
173
views
Timecourse RNASeq analysis
DESeq2
ImpulseDE2
timecour
timecoursedata
moanin
21 days ago • updated 18 days ago
Aurora
• 0
3
votes
5
replies
307
views
Help with running egsea()
EGSEA
15 days ago • updated 13 days ago
Chris
▴ 10
3
votes
4
replies
270
views
Help with error using camera() in limma
CAMERA
limma
21 days ago • updated 20 days ago
Chris
▴ 10
1
vote
4
replies
234
views
minfi::read.metharray.exp
minfiData
minfi
updated 27 days ago by
Basti
▴ 780 • written 29 days ago by
clacarion
• 0
4
votes
2
replies
643
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
19 days ago • updated 15 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
128
views
Version 3.15 S4Vectors packages are missing
S4Vectors
updated 21 days ago by
shepherl
3.9k • written 21 days ago by
bounlu
• 0
0
votes
4
replies
381
views
More regions in union when increasing DBA$config$mergeOverlap
DiffBind
updated 9 days ago by
Ziliang
• 0 • written 20 days ago by
Ian D.
▴ 70
5
votes
8
replies
8.9k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 28 days ago by
hortense96
• 0 • written 7.8 years ago by
dmcleanuk
▴ 30
1
vote
1
reply
166
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC
BatchEffect
RNASeq
updated 1 day ago by
James W. MacDonald
66k • written 1 day ago by
ttt
• 0
1
vote
1
reply
63
views
Control group between 2 batches have different expression in RNAseq data
BatchQC
BatchEffect
rnaseqGene
Normalization
updated 1 day ago by
James W. MacDonald
66k • written 1 day ago by
Đình Vinh
• 0
2
votes
9
replies
430
views
Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
DESeq2
RUVSeq
RUVseq
BatchEffect
DES
updated 25 days ago by
James W. MacDonald
66k • written 26 days ago by
Alexandre
• 0
3
votes
2
replies
241
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 29 days ago by
Guido Hooiveld
★ 4.0k • written 4 weeks ago by
fernanda.backsouza
▴ 10
1
vote
1
reply
155
views
Dominance Index for Shotgun Metagenomics Data
microbiome
updated 24 days ago by
Leo Lahti
▴ 40 • written 25 days ago by
Dario Strbenac
★ 1.5k
0
votes
2
replies
756
views
Query regarding phyloseq object construct with QIIME output
phyloseq
microbiome
Metagenomics
updated 5 days ago by
Rosso
• 0 • written 11 months ago by
abhisek001
• 0
3
votes
1
reply
1.5k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma
ebayes
bayesian
ls
updated 13 days ago by
Gordon Smyth
50k • written 5.6 years ago by
CantExitVIM
▴ 10
4
votes
9
replies
3.1k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 6 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
1
vote
3
replies
258
views
Deseq2. decontXcounts not integers. Useful alternative?
DESeq2
celda
updated 25 days ago by
Michael Love
42k • written 25 days ago by
JalapenoCornbread
• 0
0
votes
1
reply
175
views
ATACseq merge peaks
DiffBind
updated 25 days ago by
ATpoint
★ 4.1k • written 27 days ago by
Shloka
• 0
2
votes
2
replies
238
views
fgsea significant result
fgsea
16 days ago
Chris
▴ 10
2
votes
3
replies
151
views
Problem installing ChAMP on a MacBook
ChAMP
updated 5 days ago by
shepherl
3.9k • written 5 days ago by
Galia
• 0
1
vote
3
replies
265
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
Ashley
• 0
0
votes
3
replies
238
views
Couldn't connect to server while using "pathways"
graphite
updated 15 days ago by
Michael Love
42k • written 15 days ago by
fduguchunhui
• 0
0
votes
2
replies
131
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
5 days ago
makala
• 0
0
votes
3
replies
3.7k
views
[Mfuzz] Error in cmeans(exprs(eset)
Mfuzz
Mfuzz
updated 15 days ago by
Caio
• 0 • written 13.1 years ago by
boczniak767
▴ 720
0
votes
4
replies
267
views
Minfi - estimatecellscount
min
minfi
updated 22 days ago by
James W. MacDonald
66k • written 7 weeks ago by
clacarion
• 0
1
vote
2
replies
758
views
DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
DESeq2
4 weeks ago • updated 25 days ago
Patadù
▴ 10
15
votes
23
replies
2.1k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
7 weeks ago • updated 21 days ago
Chris
▴ 10
1
vote
3
replies
310
views
Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call when trying to subset pheatmap
DESeq2
updated 13 days ago by
ATpoint
★ 4.1k • written 19 days ago by
angelathuynh5
• 0
1
vote
2
replies
1.0k
views
DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, parametric = FALSE, : NA/NaN/Inf in foreign function call (arg 1)"
DMRcate
Gviz
updated 28 days ago by
Tim Peters
▴ 180 • written 14 months ago by
jose.ramirez1
▴ 10
1
vote
2
replies
218
views
Improving the design matrices vignette in RNAseq123
RNAseq123
29 days ago • updated 15 days ago
Lluís Revilla Sancho
▴ 730
1
vote
1
reply
137
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 28 days ago by
James W. MacDonald
66k • written 28 days ago by
fernanda.backsouza
▴ 10
0
votes
1
reply
165
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 8 days ago by
Guido Hooiveld
★ 4.0k • written 9 days ago by
aogunbaw
• 0
1
vote
3
replies
112
views
LRT, more than two conditions and pairwise comparisons
DESeq2
updated 23 hours ago by
James W. MacDonald
66k • written 2 days ago by
boczniak767
▴ 720
0
votes
2
replies
192
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma
RNASeq
voom
written 28 days ago by
taur.vil
• 0
0
votes
1
reply
181
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 18 days ago by
Gordon Smyth
50k • written 19 days ago by
z_bahari
• 0
1
vote
2
replies
390
views
CombineArrays for EPIC and EPIC V2
EPICV1
Methylation
combineArrays
minifi
EPICv2manifest
6 weeks ago • updated 17 days ago
Kim
• 0
0
votes
6
replies
562
views
Numerical differences in DESeq2 output depending on different design matrix construction
DESeq2
4 days ago • updated 1 day ago
Ken C
• 0
2
votes
2
replies
1.1k
views
limma for gene expression analysis with big and unbalanced sample size
limma
microarray
statistics
updated 21 days ago by
XW
• 0 • written 8.0 years ago by
tati6406
• 0
1
vote
4
replies
362
views
Opposite sign of LFC in count plots of DEGs (DESeq2)
DESeq2
27 days ago • updated 25 days ago
winwater0928
• 0
0
votes
3
replies
305
views
log2FoldChange value is way too different when compared with counts(dds)
DESeq2
updated 19 days ago by
Michael Love
42k • written 20 days ago by
HAK
• 0
2
votes
2
replies
287
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
14 days ago • updated 8 days ago
zzrammal
• 0
1
vote
4
replies
534
views
DEseq2 coefficient
DESeq2
coefficient
12 weeks ago • updated 20 days ago
JKim
• 0
4
votes
9
replies
292
views
Can DESeq2 rlog normalized matrix reflects time course result directly?
DESeq2
timecoursedata
GeneExpression
updated 5 days ago by
ATpoint
★ 4.1k • written 6 days ago by
pangtaihin
• 0
0
votes
2
replies
70
views
How to run allelic imbalance in apeglm
apeglm
updated 1 day ago by
Michael Love
42k • written 2 days ago by
euge.eugenio
▴ 20
0
votes
1
reply
267
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
CopyNumberPlots
HMMcopy
CopyNumberVariation
updated 21 days ago by
James W. MacDonald
66k • written 21 days ago by
SSSJec
• 0
0
votes
2
replies
959
views
using WGCNA, positive or negative corrlation between genes composing modules.
correlation
wgcna
network
updated 6 days ago by
mariakenneth147
• 0 • written 18 months ago by
pharamac
• 0
5
votes
6
replies
2.8k
views
Although I successfully installed the package "simpleaffy'' , I cannot library it. Why?
simpleaffy
updated 19 days ago by
James W. MacDonald
66k • written 2.4 years ago by
yanchangjian2019
• 0
2
votes
4
replies
192
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2
PCAplot
RNA-Seq
DesignModel
updated 1 day ago by
Michael Love
42k • written 4 days ago by
shaunpeterson
• 0
0
votes
1
reply
122
views
Recovering my account credentials on Bioconductor
Bioconductor
updated 14 days ago by
shepherl
3.9k • written 14 days ago by
cyril.dalmasso
• 0
178 results • Page
2 of 4
Recent ...
Replies
Answer: recount3 problem downloading data from source sra
by
Leonardo Collado Torres
★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman
by
minardsmitha
▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Answer: Documenting resources in an `ExperimentHub` package?
by
James W. MacDonald
66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
Comment: ChAMP installation issue
by
shepherl
3.9k
We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
Comment: How to arrange multiple plots into one page in NOISeq?
by
baptiste.bidon
• 0
After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
Votes
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Comment: LRT, more than two conditions and pairwise comparisons
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Awards
• All
Scholar
to
Mike Smith
★ 6.5k
Popular Question
to
mohammedtoufiq91
▴ 10
Popular Question
to
Gordon Smyth
50k
Popular Question
to
bas_work
▴ 30
Popular Question
to
landenshanie
▴ 40
Locations
• All
United States,
8 minutes ago
Germany,
35 minutes ago
Switzerland,
36 minutes ago
United States,
39 minutes ago
San Diego,
40 minutes ago
Traffic: 643 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