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12
votes
5
replies
1.9k
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News:
DOI for packages
DOI
doi
packages
citation
publication
News
6.5 years ago
shepherl
3.9k
12
votes
7
replies
4.4k
views
Plot ggplot2 and ggbio Images Together
ggplot2
ggbio
cowplot
updated 4.8 years ago by
Assa Yeroslaviz
★ 1.5k • written 8.9 years ago by
andrew.j.skelton73
▴ 370
12
votes
6
replies
4.7k
views
How to select summit size for histone ChiP-Seq in Diffbind
Diffbind
Histone Chip-Seq
Summit size
updated 24 months ago by
Rory Stark
★ 5.2k • written 6.6 years ago by
urjaswita
▴ 40
12
votes
1
reply
7.1k
views
identifying the samples on plotPCA
deseq2
plotpca
PCa
updated 6.5 years ago by
Michael Love
41k • written 6.5 years ago by
lirongrossmann
▴ 80
12
votes
13
replies
7.7k
views
EdgeR Differential Expression analysis with NAs
EdgeR
rnaseq
NA
updated 9.6 years ago by
Aaron Lun
★ 28k • written 9.6 years ago by
elliott77
• 0
12
votes
3
replies
4.9k
views
sva: how to incorporate adjusting variables
inveRsion
sva
inveRsion
sva
updated 10.7 years ago by
Jeff Leek
▴ 650 • written 10.7 years ago by
Meritxell Oliva
▴ 120
12
votes
6
replies
21k
views
DESEq2 comparison with mulitple cell types under 2 conditions
deseq2
multiple factor design
updated 9.0 years ago by
Michael Love
41k • written 9.0 years ago by
kmu004
▴ 50
12
votes
6
replies
2.6k
views
How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
edger
differential gene expression
rnaseq
updated 7.1 years ago by
Gordon Smyth
50k • written 7.1 years ago by
gabriel.rosser
▴ 20
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
12
votes
2
replies
1.4k
views
`TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed anymore
EnsDb.Hsapiens.v75
TxDb.Hsapiens.UCSC.hg19.knownGene
3.3 years ago
Batool
▴ 370
12
votes
9
replies
3.3k
views
Limma residuals matrix
limma
updated 4.7 years ago by
Gordon Smyth
50k • written 4.7 years ago by
agustin.gonvi
▴ 20
12
votes
12
replies
2.0k
views
FDR does not change between genes in edgeR
RNAseq
edgeR
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
apfelbapfel
▴ 30
12
votes
7
replies
1.9k
views
No method for coercing this S4 class to a vector, as trying to import my own data rather than using SRA in the workflow RnaSeqGeneEdgeRQL
rnaseqgeneedgerql
shortread
Rsubread
updated 5.1 years ago by
Aspie96
▴ 60 • written 5.1 years ago by
Raito92
▴ 60
11
votes
23
replies
2.6k
views
crlmm support for Illumina arrays with no annotation package?
crlmm
QCarray
annotation
updated 4.3 years ago by
milo.yanez20
• 0 • written 4.5 years ago by
deanpett
▴ 30
11
votes
3
replies
4.9k
views
WGCNA - Signed vs signed hybrid networks
wgcna
updated 7.8 years ago by
Peter Langfelder
★ 3.0k • written 7.8 years ago by
bram.verstockt
▴ 20
11
votes
16
replies
1.8k
views
Possible explanations and suggestions corresponding the interprentation of results of limma multifactorial design
limma
multifactorial design
diagnostic plots
affymetrix microarrays
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
svlachavas
▴ 830
11
votes
25
replies
11k
views
readCufflinks problem with extdata
cummerbund
updated 6.6 years ago by
markus.ball
▴ 10 • written 6.8 years ago by
biakemi
▴ 40
11
votes
8
replies
2.1k
views
Error when downloading data with recount3.
recount3
updated 2.1 years ago by
chris.wilks
▴ 70 • written 3.5 years ago by
Zach Brehm
▴ 20
11
votes
4
replies
1.7k
views
How can I find the location of a gene based on cytogenetic bands (e.g. 7q31.2)?
bioconductor
cytogenetics
updated 6.6 years ago by
Martin Morgan
25k • written 6.6 years ago by
Arman Shahrisa
▴ 20
11
votes
13
replies
4.0k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
3.4 years ago • updated 3.3 years ago
rohitsatyam102
▴ 20
11
votes
7
replies
17k
views
DESeq2: multiple conditions design -- How to select subset comparisons from the DESeq object for PCA, ...
deseq2
updated 2.5 years ago by
Michael Love
41k • written 8.1 years ago by
martin.hoelzer
▴ 20
11
votes
11
replies
15k
views
cannot install edgeR on M1 Mac
apple
m1
installation
silicon
updated 2.3 years ago by
Gordon Smyth
50k • written 2.8 years ago by
Brian
▴ 90
11
votes
10
replies
4.2k
views
Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a transcriptome?
deseq2
nanopore
5.0 years ago
David Eccles (gringer)
▴ 30
11
votes
14
replies
11k
views
Is there a conceptual difference between vst/rlog transforms and lfcShrink?
deseq2
updated 6.3 years ago by
Michael Love
41k • written 6.3 years ago by
kieran.mace
▴ 40
11
votes
21
replies
5.0k
views
How about our ATAC-Seq data quality analyzed by ATACseqQC
ATACseqQC
ATAC-Seq
quality analysis
fragment size distribution
library complexity
updated 5.2 years ago by
Julie Zhu
★ 4.3k • written 5.2 years ago by
Gary
▴ 20
11
votes
8
replies
8.6k
views
Pre-processing of RNA-Seq data for WGCNA and DGE
WGCNA
RNA-Seq
DESeq2
voom
removebatcheffect()
updated 7.6 years ago by
Peter Langfelder
★ 3.0k • written 7.6 years ago by
gokce.ouz
▴ 70
11
votes
17
replies
2.3k
views
SV4Vectors DataFrame bug with haven_labelled data
S4Vectors
DataFrame
haven_labelled
haven
updated 17 months ago by
Danny Smith
▴ 20 • written 17 months ago by
Daniel E. Weeks
▴ 30
11
votes
4
replies
33k
views
DESeq2 baseMean counts
deseq2
updated 8.4 years ago by
Michael Love
41k • written 8.4 years ago by
zpingfeng
• 0
11
votes
11
replies
3.3k
views
Different results in edgeR using simple vs GLM
edger
glm
rnaseq
8.6 years ago • updated 8.5 years ago
dietahanson
▴ 30
11
votes
5
replies
7.4k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 14 days ago by
Garrett
• 0 • written 9.1 years ago by
brohawndg
▴ 150
11
votes
1
reply
16k
views
Deseq2: RNA-seq and Negative binomial distribution
rnaseq
deseq2
updated 8.5 years ago by
Michael Love
41k • written 8.5 years ago by
tony_cybercloud
▴ 20
11
votes
15
replies
4.1k
views
Annotation for Affymetrix GeneChip PrimeView.
annotation
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 4.0 years ago by
ammasakshay
• 0
11
votes
8
replies
4.5k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps
genomicalignments
updated 9.1 years ago by
Hervé Pagès
16k • written 9.1 years ago by
rxzlmn
▴ 10
11
votes
0
replies
2.1k
views
News:
Bioconductor 3.0 is released!
news
News
9.6 years ago • updated 9.5 years ago
Dan Tenenbaum
★ 8.2k
11
votes
5
replies
3.1k
views
WGCNA with paired samples
wgcna
paired samples
exercise
updated 7.7 years ago by
Peter Langfelder
★ 3.0k • written 7.7 years ago by
2323982403
▴ 60
11
votes
4
replies
1.8k
views
LIMMA dupcor() function time issue.
limma
microarray
block
updated 7 months ago by
Gordon Smyth
50k • written 5.2 years ago by
tleona3
• 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
11
votes
5
replies
2.3k
views
Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
lumidat
idat
microarray
illumina
updated 8.6 years ago by
Mark Cowley
▴ 400 • written 8.6 years ago by
willj
▴ 30
11
votes
5
replies
4.0k
views
Scan error using biomart with version option
biomart
updated 6.3 years ago by
Mike Smith
★ 6.5k • written 6.4 years ago by
Chris Stubben
▴ 40
11
votes
1
reply
1.1k
views
News:
Rsubread now available for Windows
rsubread
News
4.7 years ago • updated 4.6 years ago
Gordon Smyth
50k
11
votes
9
replies
4.4k
views
How to remove more than two batches in my data-sets
limma
RNAseq
removebatcheffect()
updated 7.8 years ago by
Gordon Smyth
50k • written 7.8 years ago by
yi.huang
▴ 30
11
votes
0
replies
5.8k
views
Tutorial:
Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges
Annotation
RNAseq
visualization
Tutorial
8.8 years ago
Martin Morgan
25k
11
votes
9
replies
1.6k
views
Correlation of a Linear Variable
limma
limma design matrix
updated 9.1 years ago by
James W. MacDonald
65k • written 9.1 years ago by
andrew.j.skelton73
▴ 370
11
votes
14
replies
4.3k
views
Setting up the Design Matrix
rnaseq
edgeR
multiple factor design
design matrix
8.3 years ago
Yogender Gowtham
▴ 20
11
votes
15
replies
2.7k
views
edgeR - MDS Plot for Count Data
edger
DEG
mds
plot
6.7 years ago
baus87
• 0
11
votes
3
replies
1.8k
views
Fit a multinomial to RNA-seq count data
voom
limma
glm
multinomial
regression
updated 7.8 years ago by
Robert Castelo
★ 3.3k • written 7.8 years ago by
rubi
▴ 110
11
votes
20
replies
4.2k
views
Detection p-value: difference between limma and lumi packages
p-value
detection
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
Eleni Christodoulou
▴ 150
11
votes
6
replies
3.7k
views
Log fold change on Limma
limma
multiple factor design
updated 8.8 years ago by
Steve Lianoglou
★ 13k • written 8.8 years ago by
ea1402
▴ 20
11
votes
7
replies
6.3k
views
What's the rationale for using the negative binomial distribution to model read counts?
rnaseq
updated 7.8 years ago by
Ryan C. Thompson
★ 7.9k • written 7.8 years ago by
kjo
▴ 70
11
votes
14
replies
22k
views
DESeq2 normalization vs VST vs rlog
deseq2
updated 17 months ago by
Jiahua
• 0 • written 4.7 years ago by
Jonas B.
▴ 40
45,611 results • Page
4 of 913
Recent ...
Replies
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.
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0
by
Michael Love
41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i
by
James W. MacDonald
65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
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
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