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
6
votes
2
replies
708
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
9 months ago
Josué
▴ 20
6
votes
11
replies
3.9k
views
How to properly average normalized counts of biological replicates
DESeq2
Normalization
RNASeqR
updated 6 weeks ago by
Priya
• 0 • written 3.2 years ago by
Marina
▴ 40
6
votes
10
replies
2.2k
views
overlapsAny for elements in GRangesList
granges
grangeslist
overlapsAny
updated 14 days ago by
Samuel Ahuno
• 0 • written 8.0 years ago by
maltethodberg
▴ 170
6
votes
11
replies
26k
views
With DESeq2 "Not full rank" Error with design ~ line + time + condition
deseq
deseq2
updated 9 months ago by
Erika
• 0 • written 9.3 years ago by
c.lieftink@nki.nl
▴ 40
6
votes
12
replies
4.7k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
6 months ago • updated 6 days ago
shepherl
3.8k
6
votes
7
replies
556
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
aa.machado001
• 0
6
votes
7
replies
925
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
jonas.freimuth
▴ 20
6
votes
7
replies
753
views
Adding a group of samples reduces DEGs in other groups
RNASeq
limma
updated 9 months ago by
Gordon Smyth
50k • written 9 months ago by
Jonathan
▴ 10
5
votes
5
replies
434
views
create COMPOUND dataset (2 matrices) with rhdf5?
rhdf5
12 weeks ago • updated 11 weeks ago
baptiste
▴ 20
5
votes
6
replies
3.8k
views
Differential protein/biomarker expression using limma: is that possible?
Proteomics
NPX
limma
updated 3 months ago by
briankleiboeker
• 0 • written 3.1 years ago by
r.i.s.alnuwaysir
▴ 10
5
votes
6
replies
400
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 15 days ago by
ATpoint
★ 4.0k • written 19 days ago by
nhaus
▴ 30
5
votes
1
reply
426
views
News:
Bioconductor 3.18 is Released!
Packages
Bioconductor
Release
Software
written 6 months ago by
shepherl
3.8k
5
votes
8
replies
8.8k
views
Limma design with continuous and categorical covariates
limma
batch effect
covariates
microarray
updated 5 days ago by
hortense96
• 0 • written 7.7 years ago by
dmcleanuk
▴ 30
5
votes
2
replies
677
views
PhD student
TMM
limma
9 months ago
Nisha
• 0
5
votes
8
replies
3.9k
views
Problem about picking soft threshold power in WGCNA software
wgcna
rnaseq
written 7.1 years ago by
panagiotis.mokos
▴ 40
5
votes
11
replies
3.0k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 11 months ago by
Sabiha
▴ 20
5
votes
8
replies
1.4k
views
Can the limma package be applied to Log2 RUV-normalized data?
RUVnormalizeData
MicroarrayData
limma
updated 4 months ago by
Shaimaa Gamal
• 0 • written 11 months ago by
pg45863
▴ 10
5
votes
7
replies
1.0k
views
different number of DEG because of outliers
DESeq2
RNASeq
updated 3 months ago by
Gordon Smyth
50k • written 13 months ago by
Ilya
• 0
5
votes
3
replies
696
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom
blocking
limma
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
Gerhard Thallinger
▴ 180
5
votes
4
replies
381
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
10 weeks ago • updated 9 weeks ago
pl23
• 0
5
votes
7
replies
441
views
DEG Filtering
MicroarrayData
limma
Genefiltering
updated 4 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Amit
• 0
5
votes
15
replies
5.0k
views
Cross-species RNA-seq with DESeq2
deseq2
rnaseq
across species
updated 10 months ago by
James W. MacDonald
65k • written 6.8 years ago by
vtartaglio
▴ 10
5
votes
6
replies
835
views
ASpli checks fail on Linux due to missing dependency to statmod
ASpli
updated 8 months ago by
Gordon Smyth
50k • written 9 months ago by
martin.grigorov
▴ 10
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 8 months ago by
Novice_cam
• 0 • written 6.4 years ago by
knaxerova
▴ 10
5
votes
5
replies
784
views
limma output for epic array methylation data
linearregression
epicarray
MethylationArray
limma
8 months ago
Jitendra
▴ 10
5
votes
4
replies
9.7k
views
Getting rs ids using chr coordinates | Biomart
SNP
rs id
Biomart
Chromosome
coordinates
updated 9 months ago by
James W. MacDonald
65k • written 3.7 years ago by
Mahan
• 0
5
votes
2
replies
669
views
outdated GEOmetadb.sqlite
GEOmetadb
14 months ago • updated 3 months ago
Robert Castelo
★ 3.3k
5
votes
25
replies
836
views
limma models out of memory issue on Slurm HPC
Regression
limma
STATISITICS
HPC
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Jitendra
▴ 10
5
votes
1
reply
1.4k
views
Support for new Illumina human methylation EPIC array v2
human
methylationArrayAnalysis
updated 3 months ago by
s.malik
• 0 • written 13 months ago by
jenniewoo
▴ 70
5
votes
18
replies
7.5k
views
Install DESeq2 problem for macbook pro M1 Max
Bioconductor
Install
DESeq2
updated 4 months ago by
picasa1983
• 0 • written 2.2 years ago by
Victor
• 0
5
votes
2
replies
734
views
ComBat_seq function in sva package does not return a matrix
sva
ComBat
ComBat-seq
Bioconductor
ComBat_seq
7 months ago
Federico
▴ 10
5
votes
6
replies
638
views
DataFrame Construction With Non-standard Column
S4Vectors
updated 7 months ago by
Hervé Pagès
16k • written 7 months ago by
Dario Strbenac
★ 1.5k
5
votes
5
replies
1.9k
views
Archive location for Bioconductor packages
archive
updated 8 months ago by
shepherl
3.8k • written 20 months ago by
ems
▴ 20
5
votes
19
replies
5.9k
views
DiffBind GreyListChIP error: Error: BiocParallel errors
DiffBind
updated 8 months ago by
liz.lamarca
• 0 • written 2.8 years ago by
kwangbom
▴ 10
5
votes
9
replies
872
views
Light difference when using coef vs omit a group when compare 3 groups.
limma
17 days ago • updated 10 days ago
Chris
• 0
5
votes
11
replies
4.2k
views
How to annotate gene names for genomic coordinates?
annotation
written 8.9 years ago by
seeker
• 0
5
votes
3
replies
695
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Jack S.
▴ 50
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 3 months ago by
Shaimaa Gamal
• 0 • written 7.1 years ago by
myprogramming2016
• 0
5
votes
2
replies
860
views
can't install DESeq2 ("unable to access index for repository")
biocmanager
DESeq2
8 months ago
Alessia
▴ 40
5
votes
3
replies
2.0k
views
Cannot download GEOmetadb sqlite file
GEOmetadb
updated 12 weeks ago by
ilayahari
• 0 • written 6.5 years ago by
arnaud.ceol.pro
▴ 10
5
votes
9
replies
1.2k
views
Batch correction and repeated measures
RUVSeq
sva
limma
updated 10 days ago by
Gordon Smyth
50k • written 7 months ago by
Jonathan
▴ 10
5
votes
6
replies
531
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression
rnaseqGene
RNASeqData
3 months ago
Shaimaa Gamal
• 0
5
votes
2
replies
540
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
annikagable
• 0
5
votes
6
replies
1.9k
views
Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
Pigengene
5 months ago
kjngo
▴ 40
4
votes
7
replies
2.1k
views
should statmod be a dependency of limma and not a suggests?
limma
updated 9 months ago by
Gordon Smyth
50k • written 7.9 years ago by
nathan
• 0
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 3.5 years ago by
ATpoint
★ 4.0k
4
votes
2
replies
603
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
alvaroperona1
▴ 10
4
votes
2
replies
1.1k
views
metagene: paired-end bam as input
metagene
updated 5 months ago by
xlal
• 0 • written 7.5 years ago by
anton.kratz
▴ 60
4
votes
4
replies
1.2k
views
S4Vectors masking utils::findMatches is returning warnings in R 4.3 / Bioconductor 3.17
S4Vectors
written 12 months ago by
Michael Steinbaugh
▴ 90
1,730 results • Page
2 of 35
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
by
Leo Lahti
▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
Awards
• All
Popular Question
to
Leo Lahti
▴ 40
Scholar
to
James W. MacDonald
65k
Popular Question
to
shepherl
3.8k
Scholar
to
Michael Love
41k
Supporter
to
JKim
• 0
Locations
• All
Canada,
2 minutes ago
UPF, Barcelona, Spain,
17 minutes ago
India,
1 hour ago
Ireland,
1 hour ago
China,
1 hour ago
Traffic: 599 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