0
votes
1
reply
35
views
Automatically generate contrasts from a model matrix / formula
limma
updated 5 minutes ago by 51k • written 6 hours ago by ▴ 10
0
votes
2
replies
31
views
Using Normalized Counts in DESeq2
DESeq2
updated 4 hours ago by 42k • written 6 hours ago by • 0
0
votes
0
replies
10
views
DiffBind subset replicates
DiffBind
5 hours ago Haiping • 0
0
votes
0
replies
25
views
Its possible to remove annotation names using anno_simple in ComplexHeatmap
ComplexHeatmap
17 hours ago nromerov • 0
1
vote
3
replies
87
views
How to reverse complement some elements of a DNAStringSet
biostr Biostrings
written 1 day ago by • 0
1
vote
2
replies
67
views
When running contrasts, does it use normalized read counts?
DESeq2
1 day ago Katherine • 0
0
votes
0
replies
21
views
Rsubread - sublong function
pacbio sublong Rsubread
1 day ago thomas.heigl.ibk • 0
3
votes
4
replies
209
views
What should be the normalization protocol for RNA seq data for WGCNA?
RNA_seqdata Normalization_method WGCNA
1 day ago sukeshinik5 ▴ 20
1
vote
3
replies
172
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
4 days ago • updated 1 day ago yasmin.hilliam ▴ 10
0
votes
1
reply
102
views
How to adjust the DESeq2 formula when there is no control group for one factor?
DESeq2
updated 2 days ago by ★ 1.4k • written 4 days ago by • 0
1
vote
1
reply
184
views
Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringSet()
ONTdata Biostrings
2 days ago • updated 1 day ago Gerhard Thallinger ▴ 180
3
votes
3
replies
122
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
4 days ago • updated 1 day ago Guido Hooiveld ★ 4.1k
0
votes
2
replies
124
views
Need help interpreting heatmaps from limma
limma
updated 1 day ago by • 0 • written 4 days ago by • 0
0
votes
0
replies
48
views
when FOLD>0, which group of sampls increased?
BASiCS
4 days ago Jeffcgen2000 • 0
3
votes
4
replies
255
views
Are transformed values from rlog /vst log2 normalized counts?
Normalization DESeq2 rlog vst
4 days ago Eva ▴ 10
0
votes
0
replies
61
views
Deseq to output continous sequencing data
DESeq2
4 days ago Neha • 0
0
votes
0
replies
82
views
Adjusted p-values become NA when sub-setting samples
DESeq2
5 days ago txema.heredia • 0
1
vote
3
replies
271
views
Unable to install any Bioconductor package with new R 4.4.1 - path nor writable - PLEASE HELP
pathnotwritable BiocManager LEA
updated 4 days ago by 67k • written 5 days ago by ▴ 10
0
votes
0
replies
61
views
Paired splsda
mixOmics
5 days ago michelafrancesconi8 • 0
2
votes
1
reply
638
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 6 days ago by 67k • written 6 days ago by ▴ 10
0
votes
0
replies
50
views
Background normalization of Diffbind dba.normalize
Normalization DiffBind
6 days ago Young Boqin • 0
0
votes
0
replies
48
views
News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
6 days ago info ▴ 10
4
votes
4
replies
206
views
How to conduct maSigPro analysis with only one condition?
maSigPro masig
updated 5 days ago by 67k • written 6 days ago by • 0
0
votes
3
replies
245
views
Mostly increased counts in differentially accessible peaks using DESeq2
ATAC-seq DESeq2 Oddresults
12 days ago • updated 3 hours ago Ricardo Iván • 0
0
votes
1
reply
95
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 6 days ago by 42k • written 6 days ago by • 0
3
votes
11
replies
489
views
Highly DE genes but small count difference within conditions
RNASeq DESeq2 RNASeqData
written 8 days ago by • 0
0
votes
0
replies
71
views
DMRcate pcutoff setting
EpicV2 DMRcate
6 days ago kitzhu • 0
2
votes
4
replies
262
views
RNASeq Time Course Question
DESeq2 RNASeq TimeCourse
7 days ago jihoon.kim.1495 ▴ 10
0
votes
0
replies
68
views
[maser] Why does maser coverage filtering ignore skipping counts of an alt. splicing analysis?
rMATS alternativesplicing maser R
7 days ago Anke • 0
2
votes
6
replies
366
views
Annotation for EPICv2
EpicV2 ChAMPdata
7 days ago • updated 6 days ago nurkenber • 0
0
votes
1
reply
102
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 7 days ago by 42k • written 7 days ago by • 0
0
votes
1
reply
126
views
WGCNA
DEGselection RNASeqData WGCNA
updated 7 days ago by ▴ 750 • written 7 days ago by • 0
5
votes
4
replies
315
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 7 days ago by ★ 4.5k • written 12 days ago by • 0
4
votes
1
reply
196
views
edgeR 4.2.1 compression bug: a minimally reproducible snippet
edger edgeR
updated 4 days ago by 51k • written 8 days ago by • 0
2
votes
5
replies
295
views
dmpFinder for other objects
methylset minfi dmpFinder betaHMM beta
updated 6 days ago by 67k • written 8 days ago by • 0
1
vote
3
replies
288
views
GSVA ssGSEA vs. Broad implementation of ssGSEA
enrichment GSVA ssGSEA
updated 6 days ago by ★ 3.4k • written 11 days ago by ▴ 10
0
votes
1
reply
125
views
Unevaluated error in ChIPQC combined with BiocParallel
BiocParallel ChIPQC
written 9 days ago by • 0
0
votes
2
replies
200
views
RNA-Seq p value range variation
DESeq2 pvalue RNA-Seq
10 days ago paul.meraner • 0
0
votes
0
replies
114
views
News: RNAseq data analysis with Bioconductor (online course)
DESeq2 SummarizedExperiment
10 days ago info ▴ 10
2
votes
6
replies
728
views
miRTarRnaseq library
miRNATarget mirTarRnaSeq
7 months ago • updated 8 days ago María Calvo • 0
0
votes
5
replies
379
views
heatmap with batch effect
DESeq2 BatchEffect
11 days ago • updated 8 days ago tothuhien • 0
0
votes
1
reply
136
views
how do I convert an Ilumn IDREF to a CPG loci
AnnotationDbi Annotation annotation BiologicalQuestion
updated 11 days ago by 67k • written 11 days ago by • 0
0
votes
0
replies
99
views
Setting ylims in bam coverage plot and assigning compound sashimi numbers to overlay plots
Coverage Gviz sashimi
11 days ago Marco • 0
0
votes
1
reply
174
views
Which input data is acceptable for MAST?
SCTransform MAST
updated 12 days ago by ▴ 270 • written 12 days ago by • 0
1
vote
1
reply
163
views
segfault when using singleR with Azimuth reference
SingleR
updated 12 days ago by 67k • written 12 days ago by ▴ 750
0
votes
1
reply
134
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
12 days ago isaac.vock • 0
0
votes
2
replies
270
views
How can I obtain DEGs that are resulted from using salmon in alignment-based mode or mapping-based mode?
tximport DESeq2
updated 12 days ago by 42k • written 13 days ago by • 0
1
vote
1
reply
156
views
Deseq2 sfType
Microbiome DESeq2 RNASeq
updated 14 days ago by 67k • written 14 days ago by • 0
1
vote
1
reply
173
views
Normalization RNA-seq for multiple plates
Normalization DESeq2 RNASeqData edgeR
updated 14 days ago by ★ 4.5k • written 14 days ago by • 0
0
votes
1
reply
377
views
News: Subject: Last 2 Seats Available for Metabolomics with R/Bioconductor Course (October 7-10)
Metabolomics xcms
updated 13 days ago by • 0 • written 14 days ago by ▴ 10
46,090 results • Page 1 of 922
Recent ...
Replies
Answer: Automatically generate contrasts from a model matrix / formula by Gordon Smyth 51k
I am very concerned that you are attempting to extract pairwise comparisons from an interaction formula like `0 + Group*Sex + Age`, because…
Comment: Mostly increased counts in differentially accessible peaks using DESeq2 by Ricardo Iván • 0
Hi Michael, Thanks for your reply. After reviewing the PCAs, maybe the issue that despite the replicates looking similar, there is still a…
Comment: Using Normalized Counts in DESeq2 by Michael Love 42k
Also, just to add, there are many dozens of posts on this topic of DESeq2 applied to TCGA counts, normalized or other. Recommend google sea…
Answer: Using Normalized Counts in DESeq2 by ATpoint ★ 4.5k
TCGA raw counts can be obtained for example using the TCGAbiolinks or recount packages.
Comment: How to reverse complement some elements of a DNAStringSet by Christine Jones • 0
Fantastic, thank you
Votes
Answer: When running contrasts, does it use normalized read counts?
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
Awards • All
Popular Question to Michael Love 42k
Popular Question to Jonathan ▴ 10
Autobiographer to h1vu81gcd7 ▴ 20
Popular Question to nromerov • 0
Scholar to James W. MacDonald 67k
Locations • All
WEHI, Melbourne, Australia, 5 minutes ago
France, 5 minutes ago
United States, 49 minutes ago
United Kingdom, 49 minutes ago
United States, 1 hour ago
Traffic: 398 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