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NA values for DESeq2 p-values and adjusted p-values using large sample sizes
Bioconductor
4 months ago • updated 3 months ago
Gabriel
• 0
0
votes
1
reply
210
views
Gatins Set error
flowCore
Bioconductor
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
yoav.lubelsky
• 0
0
votes
1
reply
279
views
Job:
Senior Teaching Fellow (MSc Computational Biomedicine)
Bioconductor
written 4 months ago by
s.samarajiwa
• 0
0
votes
1
reply
272
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq
variancePartition
RUVSeq
limma
edgeR
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
ilaria.massaiu
• 0
0
votes
1
reply
1.0k
views
News:
Bioconductor 3.22 Release Schedule
Devel
Release
Bioconductor
written 4 months ago by
shepherl
4.3k
1
vote
11
replies
7.8k
views
DiffBind - question on the use of filtered or unfiltered input data
DiffBind
written 2.8 years ago by
Oscar
▴ 10
0
votes
2
replies
489
views
Help with defining groups
limpa
updated 23 days ago by
Gordon Smyth
53k • written 4 months ago by
Phinney, Brett
▴ 10
1
vote
2
replies
393
views
Error Loading Experiment from SimBenchData Package
Bioconductor
4 months ago
ksankaran
• 0
2
votes
4
replies
578
views
DESeq2 interactions
DESeq2
updated 3 months ago by
Michael Love
43k • written 4 months ago by
Michael
• 0
0
votes
3
replies
435
views
Sharing a collection of datasets in ExperimentHub
Bioconductor
updated 4 months ago by
Aaron Lun
★ 29k • written 4 months ago by
Stephen Piccolo
▴ 600
0
votes
3
replies
1.6k
views
problem for finding soft power for constructing network in WGCNA algorithm
RNA-seq
WGCNA package
soft power
written 7.6 years ago by
modarzi
▴ 10
0
votes
6
replies
736
views
GO.db and others package Download failure
GO.db
Bioconductor
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Skyler
• 0
0
votes
0
replies
7
views
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COSMIC.67
4 months ago
Best Rehab Center
0
2
votes
2
replies
383
views
replace cat with message in glmTreat when lfc = 0
edgeR
glmTreat
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
oliverd
• 0
0
votes
1
reply
241
views
Job:
Research and Service Group Leader positions in AI in Biology at EMBL
Bioconductor
written 4 months ago by
Wolfgang Huber
★ 13k
0
votes
1
reply
266
views
Differential motif analysis
motifmatchr
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Marek Gierlinski
▴ 30
0
votes
1
reply
379
views
News:
Ensembl 115 has been released!
ensembl
ensembldb
biomaRt
written 4 months ago by
Ensembl_Jorge
▴ 10
1
vote
3
replies
487
views
readDNAStringSet with non DNA characters
Biostrings
4 months ago
biomiha
▴ 20
0
votes
2
replies
325
views
readBam vs read_bam_insert_metrics
cfDNAPro
cfDNA
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
rtrivedi1
▴ 10
1
vote
3
replies
489
views
How to construct a BSgenome object from a custom genome assembly using BSgenomeForge?
BSgenome
BSgenomeForge
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
mat149
▴ 80
3
votes
14
replies
1.4k
views
DESeq2 used with zinbwave weights - Differences on contrasts calculations
zinbwave
DESeq2
written 6 months ago by
Aurélie
• 0
5
votes
13
replies
1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma
RNASeq
scRNAseq
updated 4 months ago by
Gordon Smyth
53k • written 4 months ago by
abaed
• 0
0
votes
1
reply
3.3k
views
Job:
Postdoctoral Research Position in Cancer Genomics at Dana-Farber Cancer Institute/Harvard University
cancer
computational biology
rnaseq
chipseq
Job
written 11.3 years ago by
gcyuan
• 0
0
votes
3
replies
438
views
Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg?
RUVSeq
DESeq2
updated 4 months ago by
Michael Love
43k • written 5 months ago by
yongjie.wang
• 0
0
votes
1
reply
868
views
Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysis of single-cell RNA-seq data?
apeglm
DESeq2
updated 5 months ago by
Michael Love
43k • written 5 months ago by
KS
• 0
0
votes
3
replies
311
views
A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::select()
org.Ss.eg.db
AnnotationDbi
written 5 months ago by
Adam Munhall
• 0
0
votes
4
replies
502
views
voomLmFit fitted log-CPM values
limma
edgeR
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
Lina
▴ 10
1
vote
3
replies
425
views
ROAST compare results with complex design
limma
mroast
roast
CAMERA
written 5 months ago by
Jiahao Tian
• 0
0
votes
0
replies
6
views
Spam:
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COSMIC.67
5 months ago
paseje6172
0
0
votes
0
replies
193
views
News:
Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
5 months ago
Ludwig Geistlinger
▴ 80
3
votes
5
replies
1.2k
views
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
DESeq2
updated 5 months ago by
James W. MacDonald
68k • written 5 months ago by
snijesh
▴ 200
0
votes
1
reply
427
views
News:
Bioconductor Board Nominations Open
TAB
Bioconductor
CAB
written 6 months ago by
shepherl
4.3k
2
votes
8
replies
827
views
Are voomByGroup and voomLmFit compatible?
limma
voomLmFit
voomByGroup
updated 5 months ago by
Gordon Smyth
53k • written 5 months ago by
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
1.3k
views
How to analyze Affy data, CEL files not available
affy
affy
written 19.0 years ago by
Bobby Prill
▴ 60
0
votes
5
replies
733
views
HMP_2019_t2d data origin
curatedMetagenomicData
updated 5 months ago by
Levi Waldron
★ 1.1k • written 6 months ago by
Blan
• 0
17
votes
45
replies
13k
views
Can NanoString data be analyzed using DESeq2?
NanoString
Differential Expressed Genes Analysis
DESeq2
updated 5 months ago by
James W. MacDonald
68k • written 6.5 years ago by
lim6432
▴ 60
3
votes
4
replies
8.5k
views
Calculation of module membership in WGCNA
WGCNA
RNA-seq
ModuleMembership
Network
Hub gene
written 5.5 years ago by
Arindam
▴ 80
0
votes
11
replies
806
views
Getting way too many DEGs with LRT for time-series RNA-seq!
TimeCourse
DESeq2
5 months ago
Denise
• 0
3
votes
4
replies
647
views
p-adjusted values in multiple comparisons
StatisticalMethod
limma
RnaSeqSampleSizeData
updated 4 months ago by
Josh
• 0 • written 5 months ago by
ocanorocabayera
• 0
2
votes
6
replies
689
views
Very different log2 Fold changes with DESeq2 and explict calculation
DESeq2
5 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
3
replies
358
views
DESeq2 inconsistent fits depending on model design with interacting factors
des
DESeq2
written 5 months ago by
fedor.bezrukov
▴ 10
0
votes
2
replies
712
views
Job:
Job: Ensembl Genebuild Project Leader
JobPosting
ensembldb
written 8 months ago by
Aleena_Ensembl
▴ 30
1
vote
2
replies
310
views
The default value of 'abundanceCol'
tximportData
6 months ago • updated 5 months ago
Jinghua
• 0
1
vote
2
replies
446
views
Testing KO vs WT at day4/day14 with interactions in edgeR
scRNAseq
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
Noah
• 0
2
votes
9
replies
1.1k
views
Transcript expression analysis in edgeR from gtf file obtained from merging long read rna-seq and standard gencode gtf
RNASeq
edgeR
LongRead
Transcript
6 months ago • updated 5 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
441
views
Difference between logFC in limma-voom and weighted limma-voom
limma
voom
weighting
6 months ago
richardallenfriedmanbrooklyn
▴ 30
0
votes
11
replies
1.1k
views
emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn
10x
scRNAseq
emptyDrops
DropletUtils
6 months ago • updated 5 months ago
Peter Hickey
▴ 760
0
votes
0
replies
6
views
Spam:
Chat GPT Gratuit
chipenrich
procoil
6 months ago
Lệ
0
3
votes
1
reply
512
views
Limpa Pipeline Order
limma
limpa
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
abadgerw
• 0
3
votes
2
replies
500
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 6 months ago by
Gordon Smyth
53k • written 6 months ago by
A.Barden
▴ 20
46,743 results • Page
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No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
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