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
2
replies
157
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
29 days ago
Marianna
▴ 20
0
votes
2
replies
183
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom
Limma
WGCNA
29 days ago
Gimena
• 0
0
votes
6
replies
330
views
unable to access Annotationhub latest record
DNAMethylation
AnnotationHub
EPICv2manifest
annotation
updated 21 days ago by
Tim Peters
▴ 170 • written 4 weeks ago by
s.malik
• 0
1
vote
10
replies
444
views
Obtaining pheno data from CEL files
GEO
affy
4 weeks ago • updated 23 days ago
Kurtis
• 0
1
vote
1
reply
150
views
DESeq2 , filter and theta arguments in resutlts()
DESeq2
4 weeks ago • updated 29 days ago
Layal
• 0
0
votes
2
replies
167
views
pca with VST of DESeq2 give 100% variance in PC1
DESeq2
sva
4 weeks ago • updated 29 days ago
michelafrancesconi8
• 0
0
votes
1
reply
140
views
Multiple affymatrix IDs mapping to a single gene name
biomaRt
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Reeya
• 0
0
votes
4
replies
253
views
Abnormal Low Dispersion Gene Population in DESeq2
DESeq2
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
Aidan
• 0
0
votes
1
reply
107
views
Brachypodium distachyon db
EnrichmentBrowser
BrachypodiumDB
RNASeqData
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
Leyre
• 0
0
votes
4
replies
414
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
4 weeks ago
Lucy
▴ 60
0
votes
2
replies
179
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
4 weeks ago
Seongsu
• 0
0
votes
1
reply
156
views
No output from read.bismark with bismark cov.files
bsseq
methylation
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
ja569116
• 0
0
votes
2
replies
174
views
Gene Ontology doubt
microbiomeExplorer
4 weeks ago • updated 28 days ago
Bhawna
• 0
0
votes
2
replies
288
views
Error in if (nrow(peaks) > 0) { : argument is of length zero Calls: CopywriteR ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous> Execution h…
CopywriteR
CopyhelpeR
4 weeks ago • updated 27 days ago
fer_talavera
• 0
1
vote
2
replies
224
views
MethylKit read issue
methylKit
updated 27 days ago by
James W. MacDonald
65k • written 4 weeks ago by
CHEN
• 0
0
votes
2
replies
252
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
4 weeks ago • updated 13 days ago
isaac.vock
• 0
0
votes
7
replies
387
views
Internet connection for Bioconductor packages in Rstudio in Iran...
No_internet_connection_Packages
Proxy
Bioconductor
GEOquery
Internet_connection_problem
4 weeks ago
needNGS
• 0
0
votes
1
reply
168
views
Convert transcriptomic bam to genomic bam?
ensembldb
transcriptome
genome
coordinateconversion
updated 4 weeks ago by
Michael Love
41k • written 4 weeks ago by
saadmurtazakhan
▴ 10
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
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
0
votes
0
replies
109
views
How to extract the coordinate of dba.plotPCA?
DiffBind
PCA
4 weeks ago
feather-W
• 0
0
votes
0
replies
109
views
PCA plot for normalized counts using Diffbind
DiffBind
PCAplot
4 weeks ago
Ankit
▴ 20
1
vote
5
replies
332
views
fgsea fork
fgsea
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
yimjohns
• 0
3
votes
5
replies
371
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Fabian
• 0
0
votes
6
replies
349
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Faisal
• 0
0
votes
1
reply
158
views
New genes that did not exist in dds object suddenly showed up after degPatterns
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Mikushi
• 0
0
votes
2
replies
226
views
WGCNA: analysis of complex trait associations with regressions
Regression
WGCNA
5 weeks ago • updated 4 weeks ago
w.cookson
• 0
0
votes
0
replies
93
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
5 weeks ago
Pierre Lindenbaum
▴ 10
0
votes
1
reply
134
views
Trimming a section of a scaffold from a genome
Biostrings
GenomeAssembly
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Karen
• 0
2
votes
3
replies
345
views
PCA of different bacterial species
DESeq2
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Laura
▴ 10
2
votes
8
replies
518
views
Microarray Limma Model fitting and DEG
limma
DGEanalysis
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
1
vote
2
replies
227
views
Problem with maplot {affy} method when using rma {affy} method output as its input
maplot_function
rma_function
ExpressionSet
MicroarrayData
affy
5 weeks ago
Mj.A.
• 0
0
votes
2
replies
205
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
SG
• 0
2
votes
2
replies
218
views
From a DNAStringSet to a data.frame
Biostrings
5 weeks ago
ramiro.barrantes
▴ 10
5
votes
25
replies
877
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 28 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Jitendra
▴ 10
0
votes
2
replies
173
views
bioconductor emailing list
Bioconductor
updated 5 weeks ago by
shepherl
3.9k • written 5 weeks ago by
1427972815
• 0
2
votes
3
replies
252
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 5 weeks ago by
Wei Shi
★ 3.6k • written 5 weeks ago by
thomas.heigl.ibk
• 0
3
votes
2
replies
210
views
How to extract counts from a DESeq dataset ordered by a specific sample?
DESeq2
Transcriptomics
5 weeks ago
Anita
▴ 10
0
votes
0
replies
116
views
Using Granges to find overlapping pairs at exactly 10kb distance
genomeIntervals
GenomicRanges
5 weeks ago
gshweta95
• 0
2
votes
1
reply
231
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 5 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
Dario Strbenac
★ 1.5k
3
votes
3
replies
389
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 5 weeks ago by
alan.ocallaghan
▴ 160 • written 5 weeks ago by
Najla Abassi
• 0
7
votes
6
replies
448
views
Batch Effect Correction, Gene Filtering
DGE
limma
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Amit
• 0
0
votes
2
replies
348
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea
gsea
5 weeks ago • updated 4 weeks ago
Gordon
• 0
2
votes
1
reply
209
views
Only positive enrichment score in GSEA
clusterProfiler
annotation
gseGO
gsea
OrgDb
updated 5 weeks ago by
Guido Hooiveld
★ 3.9k • written 5 weeks ago by
enee
▴ 10
0
votes
0
replies
139
views
News:
Deadline Extended - BioC2024 Abstracts and Sticker Contest - April 1st!
BioC2024
Conference
Bioconductor
5 weeks ago
Maria Doyle
▴ 70
1
vote
0
replies
177
views
News:
Nominations for Bioconductor Awards 2024!
Recognition
Awards
Bioconductor
Bioc204
5 weeks ago
shepherl
3.9k
0
votes
1
reply
168
views
collapseReplicates dimension error
DESeq2
Dese
updated 5 weeks ago by
Michael Love
41k • written 5 weeks ago by
Léa
• 0
0
votes
0
replies
115
views
Can i retrieve domain information from PANTHER ID's using PANTHER.db ?
PANTHER.db
5 weeks ago
nromerov
• 0
1
vote
2
replies
228
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
6 weeks ago • updated 5 weeks ago
Chanderkant Chaudhary
• 0
0
votes
1
reply
231
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 5 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
scoops_streams_06
• 0
45,611 results • Page
4 of 913
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
In that case both time and treatment are identical things, so choose one and go with it.
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
St Louis, MO,
5 minutes ago
France,
14 minutes ago
United States,
51 minutes ago
WEHI, Melbourne, Australia,
59 minutes ago
United States,
1 hour ago
Traffic: 622 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