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
15k
views
Warning message---BiocManager::install
BiocManager::install
2.7 years ago
Mengfei
• 0
2
votes
5
replies
15k
views
DESeq2: Paired Test
DESeq
DESeq2
DESeq
DESeq2
10.1 years ago • updated 10.0 years ago
Pankaj Agarwal
▴ 100
12
votes
15
replies
15k
views
WGCNA: Understanding module-trait correlations
wgcna package
updated 5.8 years ago by
Peter Langfelder
★ 3.0k • written 5.8 years ago by
bekah
▴ 40
9
votes
21
replies
15k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
updated 21 months ago by
SmallChess
▴ 10 • written 3.5 years ago by
georgia.katsoula
▴ 40
4
votes
7
replies
15k
views
package ‘edgeR’ is not available (for R version 3.1.2)
edgeR
packages
9.2 years ago
Patrick Schorderet
▴ 20
25
votes
7
replies
14k
views
Usability of ERCC spike-ins in standard RNAseq experiments
RNAseq
deseq2
ercc
updated 7.5 years ago by
Simon Anders
★ 3.7k • written 7.5 years ago by
mbeckste
▴ 30
0
votes
4
replies
14k
views
hclust(d, method = method) : NA/NaN/Inf in foreign function call (arg 10)
R
pheatmap
xcms
updated 20 months ago by
James W. MacDonald
65k • written 2.7 years ago by
onokaisaac
• 0
2
votes
4
replies
14k
views
biomaRt has encountered an unexpected server error.
biomaRt
updated 23 months ago by
Dekel
• 0 • written 4.1 years ago by
scijrb
• 0
0
votes
2
replies
14k
views
Error: install Bioconductor packages using BiocManager
software error
updated 4.5 years ago by
shepherl
3.8k • written 4.5 years ago by
mariia.kokina
• 0
8
votes
17
replies
14k
views
WGCNA for RNA-Seq Sample Set, Outliers, and Spearman correlation
WGCNA
Sample Size
Outliers
updated 8.6 years ago by
mh.manoj
• 0 • written 9.2 years ago by
brohawndg
▴ 150
21
votes
5
replies
14k
views
using duplicateCorrelation with limma+voom for RNA-seq data
limma
voom
updated 9.0 years ago by
Gordon Smyth
50k • written 9.9 years ago by
John Blischak
▴ 190
5
votes
14
replies
14k
views
How to load GEO series matrix file in R Bioconductor
geoquery
updated 8.8 years ago by
Sean Davis
21k • written 8.8 years ago by
ayanava18
▴ 10
3
votes
6
replies
14k
views
Error: Faceting variables must have at least one value when plotting with ChIPQC
ChipQC
chipqc
updated 19 months ago by
Xue
• 0 • written 7.7 years ago by
thekatybrown
▴ 10
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
3
votes
17
replies
14k
views
DESeq2 installation error
installation
updated 6.5 years ago by
Cheng-Yuan Kao
▴ 100 • written 8.7 years ago by
seeker
• 0
3
votes
11
replies
14k
views
Problems updating Bioconductor with R 3.2.0
upgrade
r update
updated 9.0 years ago by
Dan Tenenbaum
★ 8.2k • written 9.0 years ago by
daniil.sarkisyan
▴ 10
34
votes
21
replies
14k
views
DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
deseq2
9.6 years ago • updated 19 months ago
Michael Love
41k
6
votes
1
reply
14k
views
Deseq2 PCA plot customize
deseq2
pca
updated 8.3 years ago by
Michael Love
41k • written 8.3 years ago by
jarod_v6@libero.it
▴ 40
0
votes
1
reply
14k
views
operations are possible only for numeric, logical or complex types
hgu133plus2
pathview
hgu133plus2
pathview
updated 10.4 years ago by
Luo Weijun
★ 1.6k • written 10.4 years ago by
Guest User
★ 13k
3
votes
5
replies
14k
views
cannot find -llapack + -lblas for package install
lblas
llapack
LinuxMint
9.0 years ago
Eric P
▴ 10
6
votes
5
replies
14k
views
Installation of package DESeq2
deseq2
rcurl
annotate
genefilter
geneplotter
updated 7.3 years ago by
Martin Morgan
25k • written 7.3 years ago by
Rémi Willamme
▴ 10
2
votes
13
replies
14k
views
Issues connecting with R 3.2.2 to source("http://bioconductor.org/biocLite.R")
spade
8.5 years ago
frostbite907
• 0
14
votes
4
replies
14k
views
WGCNA Hub Gene Selection Method
WGCNA
Hub Genes
KmE
Intramodular Connectivity
updated 8.8 years ago by
Peter Langfelder
★ 3.0k • written 8.8 years ago by
brohawndg
▴ 150
0
votes
5
replies
14k
views
cannot open file './', reason 'Permission denied' in: file(file, "r")
updated 16.7 years ago by
Wolfgang Huber
★ 13k • written 16.7 years ago by
mete@seas.upenn.edu
▴ 50
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
0
votes
1
reply
14k
views
error under "hclust" for expression data
Clustering
Clustering
updated 12.0 years ago by
James F. Reid
▴ 610 • written 12.0 years ago by
Wang, Li
▴ 180
5
votes
8
replies
14k
views
Ensembl site unresponsive
ensembl
biomart
updated 3.0 years ago by
tommaso.gastaldi
• 0 • written 3.5 years ago by
lirongrossmann
▴ 40
1
vote
13
replies
14k
views
Count matrix from Kallisto as input for DESeq2
rnaseq
deseq2
kallisto
7.7 years ago • updated 7.6 years ago
yjliu1127
• 0
6
votes
4
replies
14k
views
EdgeR Design matrix not of full rank
edger
updated 8.9 years ago by
Gordon Smyth
50k • written 8.9 years ago by
kjclowers
• 0
1
vote
13
replies
14k
views
GeneList issue ClusterProfiler
genelist
clusterprofiler
6.9 years ago
bhgyu
▴ 30
13
votes
20
replies
14k
views
Can I feed TCGA normalized count data to EdgeR for differential gene expression analysis
EdgeR
TCGA
normalized count
updated 9.1 years ago by
alakatos
▴ 130 • written 9.1 years ago by
ycding
▴ 10
4
votes
1
reply
14k
views
The latest version of R is 3.5.1 and it is not compatible with many Bioconductor packages.
R
deseq
tcgabiolinks
5.7 years ago
ansari.sarabio
• 0
11
votes
5
replies
13k
views
Limma: how to get same output as topTable but for all the genes ?
limma
toptable
updated 6.8 years ago by
Gordon Smyth
50k • written 15.4 years ago by
Daren Tan
▴ 190
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 22 months ago by
Mohamed
▴ 30
2
votes
12
replies
13k
views
Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
flowcore
spillover
updated 6.4 years ago by
Jiang, Mike
★ 1.3k • written 6.4 years ago by
biomiha
▴ 20
0
votes
3
replies
13k
views
Problem installing tximportData
tximportdata
7.1 years ago
elg
• 0
3
votes
1
reply
13k
views
convert data in to expression set
limma
convert
limma
convert
updated 10.9 years ago by
Jeremy Ng
▴ 180 • written 10.9 years ago by
Nikul Soni
▴ 80
0
votes
9
replies
13k
views
edgeR warnings and then error
edgeR
edgeR
updated 11.5 years ago by
Gordon Smyth
50k • written 11.5 years ago by
john herbert
▴ 560
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
2
votes
4
replies
13k
views
biomartRt: convert mouse gene symbol return multiple human gene symbol
biomart
gene symbol
updated 8.8 years ago by
Diego Diez
▴ 760 • written 8.9 years ago by
chang02_23
▴ 30
0
votes
4
replies
13k
views
Normalization by DEseq
Genetics
Normalization
DESeq
Genetics
Normalization
DESeq
updated 6.2 years ago by
diannedai
• 0 • written 13.5 years ago by
Rui Luo
▴ 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
3
votes
4
replies
13k
views
[GenomicRanges] subsetByOverlaps to keep info from both GRanges objects?
updated 10.7 years ago by
Valerie Obenchain
★ 6.8k • written 10.7 years ago by
enricoferrero
▴ 660
3
votes
3
replies
13k
views
How to fix 'long vectors not supported yet' error in R
r
updated 24 days ago by
Amruta
• 0 • written 5.2 years ago by
r.tor
• 0
3
votes
4
replies
13k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart
error
ensembldb
6.2 years ago • updated 6.1 years ago
Yuqia
• 0
0
votes
5
replies
13k
views
Error:The design matrix has the same number of samples and coefficients to fit, so estimation of dispersion is not possible. Treating samples as …
deseq2
updated 2.1 years ago by
sunnet.ys
• 0 • written 3.6 years ago by
takisliako
• 0
0
votes
7
replies
13k
views
Applying DESeq on RSEM output
edgeR
DESeq
edgeR
DESeq
updated 3.1 years ago by
mehdimerbah
• 0 • written 11.1 years ago by
dvir.tau@gmail.com
▴ 30
0
votes
1
reply
13k
views
Problem with installation of org.Hs.eg.db
software error
org.hs.eg.db
updated 7.5 years ago by
Jenny Drnevich
★ 2.0k • written 7.5 years ago by
sven.schuierer
• 0
10
votes
4
replies
13k
views
Removing batch effect with limma::removeBatchEffect() actually exacerbates the effect
limma
deseq2
updated 4.9 years ago by
Gordon Smyth
50k • written 4.9 years ago by
drowsygoat
▴ 30
4
votes
5
replies
13k
views
DGEList error ?
DATA import
updated 6.1 years ago by
yusheng_tan
• 0 • written 6.5 years ago by
Björn
• 0
45,581 results • Page
4 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
United States,
10 minutes ago
WEHI, Melbourne, Australia,
22 minutes ago
India,
1 hour ago
China,
1 hour ago
Singapore,
3 hours ago
Traffic: 497 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