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0
votes
4
replies
298
views
Unable to annotate ExpressionSet object from hugene11st chip
oligo
limma
hugene11stprobeset.db
AffymetrixChip
10 days ago • updated 2 days ago
Efra
• 0
5
votes
4
replies
286
views
Estimating Cell Counts for EPIC V2 array data
FlowSorted.Blood.EPIC
minifi
28 days ago • updated 27 days ago
Kim
• 0
4
votes
4
replies
1.0k
views
Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
DESeq2
Dese
DifferentialRegulation
differe
updated 13 days ago by
feather-W
• 0 • written 11 months ago by
Bernardo
▴ 10
11
votes
4
replies
7.2k
views
Theoretical WGCNA Question
WGCNA
Theory
Scale-Free Topology
updated 1 day ago by
Peter Langfelder
★ 2.9k • written 9.0 years ago by
brohawndg
▴ 150
1
vote
3
replies
2.9k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 9 days ago by
snijesh
▴ 20 • written 6.5 years ago by
Ramiro Magno
▴ 100
1
vote
3
replies
259
views
DESEQ2 Batch Effect
DESeq2
BatchEffect
RNASeq
updated 24 days ago by
swbarnes2
★ 1.3k • written 26 days ago by
sap275
▴ 10
0
votes
3
replies
2.2k
views
internal error in trio library when trying to use lfmm() in LEA package
lfmm
LEA
updated 4 days ago by
m.charters
• 0 • written 2.9 years ago by
valentinarov
• 0
0
votes
3
replies
555
views
diffbind analyze for wheat
DiffBind
updated 28 days ago by
Igor
• 0 • written 6 months ago by
zgyu12
• 0
0
votes
3
replies
535
views
SingleR Label.Ont
SingleR
written 6 months ago by
saeed.khalili
• 0
0
votes
3
replies
212
views
Differential enrichment analysis
limma
Differentialenrichmentanalysis
DEP
updated 22 days ago by
Gordon Smyth
50k • written 29 days ago by
Laura
• 0
0
votes
3
replies
1.1k
views
GDCprepare : Error: BiocParallel errors/Error in stopAndCache(title):
BiocParallelerrors
updated 28 days ago by
Siri
• 0 • written 17 months ago by
shuangshuang
• 0
0
votes
3
replies
177
views
Help with Complex DESeq2 Design
DESeq2
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
kelsey.beavers
• 0
1
vote
3
replies
315
views
DEseq2 coefficient
DESeq2
coefficient
4 weeks ago • updated 12 days ago
JKim
• 0
0
votes
3
replies
366
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 11 weeks ago by
Fayrouz
• 0
2
votes
3
replies
378
views
"could not find function "readTSGE" in package ctsGE" Error occurs when trying to follow ctsGE package instructions.
GeneExpression
Clustering
ctsGE
4 weeks ago • updated 29 days ago
jbgnielson
• 0
0
votes
3
replies
152
views
PCA of different bacterial species
DESeq2
updated 1 day ago by
Michael Love
41k • written 1 day ago by
Laura
▴ 10
0
votes
3
replies
1.3k
views
Error in ImportRData
dplyr
IsoformSwitchAnalyzeR
written 11 months ago by
ramon.dslps
• 0
4
votes
3
replies
163
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb
gmt
GSEA
written 10 days ago by
Georg
• 0
1
vote
3
replies
173
views
miRTarRnaseq library
miRNATarget
mirTarRnaSeq
updated 17 hours ago by
mercedeh.movassagh
▴ 10 • written 9 days ago by
María
• 0
0
votes
3
replies
216
views
impute.knn produces different results based on matrix order
impute
updated 28 days ago by
James W. MacDonald
65k • written 29 days ago by
Tamara
• 0
2
votes
3
replies
217
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 days ago by
Gordon Smyth
50k • written 10 days ago by
JKim
• 0
2
votes
3
replies
135
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 2 days ago by
Wei Shi
★ 3.6k • written 3 days ago by
thomas.heigl.ibk
• 0
2
votes
3
replies
2.1k
views
Fail BiocManager::install(version='3.12')
BioManager
updated 12 days ago by
ATpoint
★ 4.0k • written 24 months ago by
liqidong52
▴ 20
1
vote
3
replies
245
views
Dispersion estimation step is very slow with latest DESeq2 and glmGamPoi
DESeq2
glmGamPoi
28 days ago • updated 22 days ago
I-Hsuan Lin
▴ 10
4
votes
3
replies
390
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 21 hours ago by
Gordon Smyth
50k • written 7 days ago by
Jack S.
▴ 50
0
votes
3
replies
1.1k
views
Blacklist error in DiffBind
DiffBind
Blacklist
updated 19 days ago by
marram_wang
• 0 • written 16 months ago by
Romain
• 0
1
vote
3
replies
222
views
DESeq2 - Plot Nr. Genes vs Variance explained in PCA
DESeq2
updated 7 days ago by
Michael Love
41k • written 10 days ago by
andrebolerbarros
▴ 20
0
votes
3
replies
225
views
Would I treat surrogate variables as batches?
DESeq2
sva
updated 24 days ago by
James W. MacDonald
65k • written 27 days ago by
MEME
▴ 10
1
vote
3
replies
180
views
cBioPortalData loads empty z-score expression table
cBioPortalData
updated 6 days ago by
Marcel Ramos
690 • written 7 days ago by
Astrid Deschênes
• 0
0
votes
3
replies
306
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 8 weeks ago by
pl23
• 0
1
vote
3
replies
192
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 3 days ago by
alan.ocallaghan
▴ 150 • written 4 days ago by
Najla Abassi
• 0
0
votes
2
replies
264
views
News:
List of Deprecated Packages for Bioc3.19
Release
Devel
ExperimentData
Software
28 days ago • updated 16 days ago
shepherl
3.8k
0
votes
2
replies
1.0k
views
News:
European Bioconductor Conference 2023 planning
Europe
Conference
EuroBioC
Events
News
updated 9 days ago by
william
• 0 • written 17 months ago by
Maria Doyle
▴ 70
0
votes
2
replies
398
views
help checking the design matrix and contrast in DESeq2 "not full rank" scenario
DESeq2
6 weeks ago • updated 29 days ago
ccshao
▴ 70
1
vote
2
replies
224
views
Impute does not work
impute
4 weeks ago • updated 29 days ago
Laura
• 0
1
vote
2
replies
185
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
21 days ago
thomas
• 0
2
votes
2
replies
184
views
padj-based gradient scale from barplot (clusterProfiler results) does not work properly
enrichplot
barplot
clusterProfiler
10 days ago
Eva
▴ 10
1
vote
2
replies
617
views
gds in GEOmetadb 2023-06-26 version is empty
GEOmetadb
written 8 months ago by
malat1_t
▴ 10
1
vote
2
replies
158
views
Extracting genomic sequences using agat and bedtools yields different results
MAST
updated 8 days ago by
ATpoint
★ 4.0k • written 9 days ago by
maximilian.beikirch
• 0
2
votes
2
replies
187
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
14 days ago
Sabiha
▴ 20
0
votes
2
replies
293
views
Is DESeq2 normalisation appropriate when counts were obtained for a small number of genes?
DESeq2
updated 26 days ago by
ATpoint
★ 4.0k • written 28 days ago by
Suvi
• 0
2
votes
2
replies
99
views
From a DNAStringSet to a data.frame
Biostrings
2 days ago
ramiro.barrantes
▴ 10
1
vote
2
replies
128
views
DESeq2 "Contrast" option
DESeq2
contrast
DifferentialExpression
7 days ago • updated 1 day ago
Chanderkant Chaudhary
• 0
0
votes
2
replies
1.2k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 17 days ago by
leedakyung1998
• 0 • written 2.6 years ago by
MP
• 0
0
votes
2
replies
1.0k
views
error when using M-values in ChAMP
ChAMP
updated 5 hours ago by
hortenseguillaume96
• 0 • written 6.2 years ago by
a.mcneill
• 0
0
votes
2
replies
97
views
Clarification on Library Size Normalization After Using tximport with countsFromAbundance="lengthScaledTPM"
tximport
updated 2 days ago by
Michael Love
41k • written 2 days ago by
SG
• 0
2
votes
2
replies
197
views
between lane normalization upper quantile
EDASeq
edgeR
14 days ago • updated 10 days ago
elesofi
• 0
0
votes
2
replies
148
views
arm64 Update to flowWorkspace (4.14.2)
flowWorkspace
28 days ago
rgong1
• 0
0
votes
2
replies
247
views
Missing Band on Volcano Plot from DESeq2
DESeq2
Visualization
DifferentialExpression
updated 14 days ago by
Michael Love
41k • written 15 days ago by
gglatzer
• 0
0
votes
2
replies
135
views
Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
9 days ago • updated 8 days ago
rocanja
▴ 60
192 results • Page
2 of 4
Recent ...
Replies
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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