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
18
votes
4
replies
1.6k
views
`ggbio` package can't be loaded
ggbio
3.3 years ago
Batool
▴ 370
18
votes
4
replies
33k
views
FDR and padj in deseq and edger
deseq2
edger
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
tonja.r
▴ 80
18
votes
17
replies
4.0k
views
How to model a comparison between comparisons in edgeR?
edger
rnaseq
updated 9.1 years ago by
Ryan C. Thompson
★ 7.9k • written 9.1 years ago by
Nick N
▴ 60
18
votes
24
replies
14k
views
[DESeq2] time series strain-specific differences over time
deseq2
timecourse
updated 3.2 years ago by
ethicalhackers
• 0 • written 9.1 years ago by
john
▴ 120
18
votes
12
replies
3.7k
views
Low-count filtering with uneven sequencing depth between samples?
edgeR
deseq2
rna-seq
independent filtering
updated 8.9 years ago by
Michael Love
41k • written 8.9 years ago by
Ryan C. Thompson
★ 7.9k
17
votes
7
replies
11k
views
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
deseq2
ensembl
updated 6.2 years ago by
James W. MacDonald
65k • written 6.2 years ago by
casey.rimland
▴ 150
17
votes
7
replies
5.9k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma
removebatcheffect
deseq2
updated 7.9 years ago by
Ryan C. Thompson
★ 7.9k • written 7.9 years ago by
ompandey
▴ 10
17
votes
8
replies
3.1k
views
How to check the read length for all the TCGA data samples in GDC?
gdc
tcga
wes
gdc data
updated 6.0 years ago by
Sean Davis
21k • written 6.0 years ago by
Biologist
▴ 110
17
votes
5
replies
4.1k
views
Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
IRanges
updated 7.2 years ago by
Martin Morgan
25k • written 7.2 years ago by
mdoering
▴ 20
17
votes
14
replies
40k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq
differential gene expression
logfc
limma
R
updated 22 months ago by
OE
• 0 • written 6.8 years ago by
cms72
▴ 20
17
votes
7
replies
13k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2
lfc
coef
contrast
updated 6.7 years ago by
Michael Love
41k • written 6.7 years ago by
Anke Busch
▴ 10
17
votes
4
replies
9.0k
views
Tutorial:
Updated Support Site Editor
support.bioconductor.org
editor
markdown
updates
Tutorial
updated 4 weeks ago by
Mj.A.
• 0 • written 5.2 years ago by
shepherl
3.8k
17
votes
4
replies
16k
views
How to properly sort GRanges?
granges
genomicranges
sort
seqnames
order
updated 9.0 years ago by
yinghua
▴ 30 • written 9.5 years ago by
enricoferrero
▴ 660
17
votes
8
replies
11k
views
remove microarray batch effects using Limma
Microarray
updated 2.7 years ago by
Leanne
• 0 • written 13.5 years ago by
Xie, Zhi NIH/NHLBI [E]
▴ 120
17
votes
4
replies
30k
views
RPKM, CPM and TMM
edger
rnaseq
differential expression
updated 8.8 years ago by
Aaron Lun
★ 28k • written 8.8 years ago by
Pauly Lin
▴ 150
17
votes
9
replies
32k
views
DESeq2 and shrinkage of log2 fold changes
deseq2
updated 3.3 years ago by
Michael Love
41k • written 8.3 years ago by
ribioinfo
▴ 100
17
votes
5
replies
4.8k
views
limma voom Mean-variance trend plot: x-axis?
limma
5.0 years ago
AS
▴ 70
16
votes
5
replies
7.4k
views
DESeq and Limma+Voom Normalization for Rna-Seq Data Using Ercc Spike-In
limma
voom
deseq
normalization
ercc
updated 8.4 years ago by
Gordon Smyth
50k • written 8.4 years ago by
komal.rathi
▴ 120
16
votes
25
replies
3.0k
views
dtuScaledTPM vs lengthScaledTPM in DTU analysis
tximport
dtu
salmon
TPM
rnaseqDTU
written 5.1 years ago by
fiona.dick91
▴ 60
16
votes
13
replies
4.4k
views
Camera and ROAST
limma
updated 6.4 years ago by
Gordon Smyth
50k • written 6.4 years ago by
Nuno Pires
▴ 30
16
votes
0
replies
3.7k
views
simultaneous use of robust and weighting methods in limma
limma
robust
arrayWeights
10.4 years ago • updated 7.9 years ago
Gordon Smyth
50k
16
votes
12
replies
2.3k
views
VST transformation (DESeq2) for metabolomics data
vst
Metabolomics
DESeq2
2.0 years ago • updated 24 months ago
Joan Miró
▴ 80
16
votes
5
replies
14k
views
Error: Bioconductor version '3.8' requires R version '3.5'
software error
updated 5.0 years ago by
Mike Smith
★ 6.5k • written 5.0 years ago by
romanowska.j
▴ 10
16
votes
13
replies
16k
views
deseq2 normalized data with heatmap
deseq2
updated 2.8 years ago by
Ian
▴ 10 • written 3.7 years ago by
linouhao
▴ 20
16
votes
4
replies
11k
views
How to use GenomicRanges to find overlaps by percentage covered of interval
genomicranges
updated 8.6 years ago by
Michael Lawrence
★ 11k • written 8.6 years ago by
khauser130d
▴ 50
16
votes
10
replies
6.7k
views
Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE
GenomeInfoDb
updated 15 months ago by
Hervé Pagès
16k • written 2.5 years ago by
sarah.howles
▴ 20
16
votes
40
replies
8.5k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 2.3 years ago by
Clara
• 0 • written 4.8 years ago by
lim6432
▴ 50
16
votes
9
replies
6.5k
views
Diffbind: edgeR or DESeq2 ?
diffbind
medip-seq
edger
deseq2
updated 6.5 years ago by
Rory Stark
★ 5.2k • written 8.1 years ago by
florian.noack
▴ 60
15
votes
2
replies
17k
views
Extract sequence from DNAStringSet object
dnastringset
updated 8.5 years ago by
Martin Morgan
25k • written 8.5 years ago by
komal.rathi
▴ 120
15
votes
9
replies
13k
views
Best way to convert uniprot accessions to entrez gene identifiers in R
org.hs.eg.db
uniprot accessions
entrez gene identifiers
updated 8.7 years ago by
James W. MacDonald
65k • written 8.7 years ago by
Aditya
▴ 160
15
votes
14
replies
3.6k
views
extract similar expressed genes (SEGs) rather than DEGs
limma
microarray
updated 9.2 years ago by
Sean Davis
21k • written 9.3 years ago by
Andreas Heider
▴ 340
15
votes
6
replies
3.2k
views
Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE methods?
edgeR
limma
diffSplice
DEXSeq
updated 7.7 years ago by
Charity Law
▴ 90 • written 7.7 years ago by
maltethodberg
▴ 170
15
votes
6
replies
29k
views
How does edgeR cpm function calculate log(CPM) values?
edgeR
cpm
updated 5.9 years ago by
ftroot1010
▴ 20 • written 6.1 years ago by
jxb.dev
▴ 40
15
votes
3
replies
1.6k
views
lfcShrink function for different comparison
DESeq2
RNASeq
updated 2.2 years ago by
molly_the_minotaur
▴ 30 • written 3.5 years ago by
bi.mi
▴ 90
15
votes
17
replies
23k
views
WGCNA: What is `soft thresholding`?
wgcna
network analysis
network
correlation
coexpression
updated 3.4 years ago by
Lluís Revilla Sancho
▴ 730 • written 7.6 years ago by
jol.espinoz
▴ 40
15
votes
13
replies
3.0k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 2.5 years ago by
xiang
▴ 10 • written 2.5 years ago by
immuno.dh
▴ 20
15
votes
4
replies
32k
views
Error in DESeqDataSet : some values in assay are not integers
deseq2
metagenomics
updated 3.7 years ago by
Ram
▴ 190 • written 3.7 years ago by
c.e.chong
▴ 10
15
votes
12
replies
66k
views
[DESEQ2] How to access the normalized data of a DESeqDataSet
deseq2
updated 9.1 years ago by
Steve Lianoglou
★ 13k • written 9.1 years ago by
john
▴ 120
15
votes
4
replies
11k
views
How to convert a GRangesList object into a GRanges object?
genomicranges
grangeslist
granges
s4
updated 2.1 years ago by
Hervé Pagès
16k • written 7.9 years ago by
richierocks
▴ 40
15
votes
18
replies
3.3k
views
Is goana function for Gene Ontology enrichement analysis suitable for both edgeR and DESeq2 DEGs lists?
DESeq2
edgeR
goana
GO
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Raito92
▴ 60
15
votes
22
replies
1.8k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
29 days ago • updated 7 days ago
Chris
• 0
15
votes
8
replies
11k
views
DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
deseq2
deseq
9.5 years ago • updated 9.4 years ago
salahm
▴ 70
15
votes
4
replies
2.7k
views
Using multiple tools for differential gene expression analysis as validation
edger
limma
deseq2
rnaseq
updated 7.8 years ago by
Ryan C. Thompson
★ 7.9k • written 7.8 years ago by
WouterDeCoster
▴ 130
15
votes
12
replies
2.5k
views
ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like they should be markers
deseq2
ZINB-WaVE
single cell
RNA-seq
differential expression
updated 5.7 years ago by
Michael Love
41k • written 5.7 years ago by
rory.kirchner
▴ 60
14
votes
10
replies
3.7k
views
Error when trying to preprocessReads() : "Error: logical subscript contains NAs"
systempiper
5.4 years ago
Deleted
▴ 70
14
votes
16
replies
2.7k
views
TopTable Problem : Unique Adj.P.Val which is near 1
limma
toptable
7.9 years ago
giroudpaul
▴ 40
14
votes
19
replies
19k
views
DESeq2: add annotations (from data frame) to DESeqDataSet
deseq2
annotation
granges
updated 2.2 years ago by
Nadine
▴ 60 • written 9.5 years ago by
Darya Vanichkina
▴ 120
14
votes
12
replies
9.3k
views
limma lmFit coefficients and p-values
limma
methylation
ewas
updated 7.7 years ago by
Steve Lianoglou
★ 13k • written 7.7 years ago by
CPR
▴ 30
14
votes
21
replies
11k
views
Installing ShortRead - error: zlib not found even with zlib in LD_LIBRARY_PATH
package installation
shortread
dependency
updated 4.9 years ago by
January Weiner
▴ 240 • written 6.0 years ago by
joseph.elsherbini
▴ 60
14
votes
8
replies
2.6k
views
News:
Bioconductor packages now each have a DOI.
doi
citation
News
updated 6.6 years ago by
Martin Morgan
25k • written 6.7 years ago by
Sean Davis
21k
45,581 results • Page
2 of 912
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
France,
1 minute ago
UPF, Barcelona, Spain,
12 minutes ago
WEHI, Melbourne, Australia,
13 minutes ago
The city by the bay,
15 minutes ago
United States,
24 minutes ago
Traffic: 463 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