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1.2k
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Pre-filtering TPM kallisto for ssGSEA / DESeq2
tximport
DESeq2
GSVA
13 months ago
georgii.vdovin
• 0
0
votes
1
reply
938
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
updated 13 months ago by
Gordon Smyth
53k • written 22 months ago by
chris2.a.white
• 0
0
votes
0
replies
10
views
Spam:
Best Hotels In Maui
prebs
13 months ago
2zrcj3448p
0
0
votes
1
reply
9
views
Spam:
Small Business Directory Emerald Coast
BUScorrect
offtopic
updated 13 months ago by
shepherl
4.3k • written 13 months ago by
2zrcj3448p
0
6
votes
5
replies
2.3k
views
MEDIPS for chIP-Seq
ChIPSeq
written 3.4 years ago by
Darek
▴ 30
0
votes
1
reply
437
views
Matching patterns in an AAStringset
Biostrings
updated 13 months ago by
Aidan
▴ 70 • written 13 months ago by
Cédric
• 0
0
votes
2
replies
780
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma
DifferentialExpression
Designmatrix
13 months ago
Tadeoye
▴ 20
0
votes
7
replies
1.4k
views
DESeq2: Gene is DEG in one experiment but not in the other depite similar baseMean, L2FC, ...
DESeq2
updated 13 months ago by
txema.heredia
• 0 • written 13 months ago by
fjrsa
• 0
2
votes
4
replies
994
views
Can we get beta values with DMRcate package
DMRcatedata
DMRcate
13 months ago
Melisa Tecik
• 0
2
votes
2
replies
864
views
Running multiple KNN queries in parallel
BiocParallel
BiocNeighbors
13 months ago
SamGG
▴ 360
5
votes
4
replies
1.5k
views
RSubread output significantly different from bash Subread output
Subread
Rsubread
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
Aimee
▴ 10
0
votes
0
replies
529
views
Job:
Postdoc/Staff Scientist Position at UT Southwestern Medical Center
PathologyData
LungCancerData
JobPosting
13 months ago
cailing20
• 0
0
votes
1
reply
584
views
Deseq2 Error in solve.default(qr.R(qrx)) : 'a' (1 x 0) must be square
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
bhandary.8590
▴ 20
0
votes
2
replies
998
views
sva: get a sv for RIN scores
limma
sva
variancePartition
voom
RNASeq
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Lina
▴ 10
0
votes
2
replies
558
views
git push errors
RiboDiPA
13 months ago
Jiping Wang
▴ 90
2
votes
3
replies
1.9k
views
How to annotate a limma Elist raw class object with an annotation file
limma
AnnotationDbi
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
giulia.gentile
▴ 10
0
votes
3
replies
814
views
DESeq2 - Comparing Comparisons
DESeq2
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
sk
• 0
0
votes
0
replies
305
views
Confidence interval contains 0 but p<0.05
MAST
13 months ago
Adelyn
• 0
0
votes
4
replies
1.0k
views
lfcShrink and alpha value
lfcShrink
DESeq2
13 months ago
anon
• 0
0
votes
0
replies
490
views
Pathway abundance data from Curatedmetagenomics
curatedMetagenomicData
ExperimentHubData
13 months ago
Edward
• 0
1
vote
4
replies
1.0k
views
pathview - multiple states
pathview
Pathways
KEGG
13 months ago
Philippine
• 0
2
votes
5
replies
1.2k
views
scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data
scuttle
updated 13 months ago by
Aaron Lun
★ 29k • written 13 months ago by
Adam
▴ 10
1
vote
2
replies
765
views
contrast matrix design for a continuous variable
limma
13 months ago • updated 12 months ago
dtzhu337
• 0
2
votes
1
reply
803
views
DESeq2- merging technical vs biological replicates
DESeq2
RNASeqData
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Nikita
• 0
0
votes
2
replies
540
views
DESeq2 dispersion estimates fitting drastically different based on explanatory variable scaling
dispersionestimates
DESeq2
updated 13 months ago by
Michael Love
43k • written 13 months ago by
Sam
• 0
0
votes
5
replies
795
views
fail to use addPerROIQC in Rmd
stand
standR
updated 13 months ago by
liu.n
• 0 • written 13 months ago by
joseph.joonsang
• 0
4
votes
8
replies
2.0k
views
how to apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
DMRcate
minfi
13 months ago • updated 11 months ago
xiaofeiwang198266
• 0
3
votes
3
replies
1.1k
views
Crossover design with limma
limma
crossover
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Marek Gierlinski
▴ 30
0
votes
9
replies
1.9k
views
Differential Expression Genes as Independent Variables
limma
DifferentialExpression
variancePartition
dream
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
abadgerw
• 0
6
votes
10
replies
3.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
mohammedtoufiq91
▴ 10
0
votes
1
reply
571
views
rrvgo::calculateSimMatrix() error
rrvgo
updated 13 months ago by
Phila
• 0 • written 13 months ago by
Michelle
• 0
0
votes
0
replies
457
views
Job:
3x PhD positions in UK: cool algorithms and impactful applications
JobPosting
13 months ago
Daphne
• 0
0
votes
2
replies
523
views
DESeq2 sizefactors counfounded with biological treatment
DESeq2
13 months ago
Anna
• 0
2
votes
1
reply
1.1k
views
bioconductor packages on bioconda
Bioconductor
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
risch.vinzent
• 0
1
vote
4
replies
701
views
txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
TxDb.Mmusculus.UCSC.mm10.ensGene
TxDb
karyoploteR
13 months ago
remi-xavier.coux
▴ 10
1
vote
2
replies
595
views
Epic v2 Annotation CpG_maf source?
MethylationArray
methy
EPICv2manifest
13 months ago
Meghan
• 0
1
vote
3
replies
852
views
Struggle with the replicates of epic array data
limma
epicarray
IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 13 months ago by
Melisa Tecik
• 0
0
votes
0
replies
402
views
Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization
Lipidomics
lipidr
13 months ago
David R
▴ 90
0
votes
0
replies
5
views
Spam:
<img/src/onerror=alert(1337)>
genomes
rgu34cprobe
13 months ago
<img/src/onerror=alert(1337)>
0
1
vote
2
replies
835
views
Deseq2 res Function
DESeq2
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
sap275
▴ 10
7
votes
6
replies
1.5k
views
ANOVA like approach of edgeR
edgeR
updated 13 months ago by
Gordon Smyth
53k • written 13 months ago by
Talip
▴ 10
0
votes
2
replies
754
views
Create Illmina bead summary data
beadarray
Illuminabeadchip
GenomeStudio
lumi
13 months ago
Liu
• 0
0
votes
4
replies
798
views
Help with RSEM counts: do I transpose matrix?
RSEM
DESeq2
13 months ago
NB
• 0
0
votes
1
reply
780
views
WGCNA with TPM tables
RNASeq
WGCNA
ComparativeGenomics
updated 13 months ago by
ATpoint
★ 5.0k • written 13 months ago by
siobhan.dietz
• 0
2
votes
5
replies
2.3k
views
Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ("trying to load regions beyond the boundaries of non-circular sequenc…
genomes
BSgenome.Mmusculus.UCSC.mm39
updated 13 months ago by
James W. MacDonald
68k • written 13 months ago by
Paul
• 0
0
votes
5
replies
801
views
Identical samples after deseq2 batch effect removal
DESeq2
updated 13 months ago by
Michael Love
43k • written 14 months ago by
maripane
• 0
0
votes
1
reply
616
views
DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Raya
• 0
1
vote
1
reply
735
views
BiocNeighbours Utility for k-Nearest Neighbour Classification
Classification
BiocNeighbors
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
Dario Strbenac
★ 1.6k
0
votes
1
reply
434
views
HilBertVis install error
HilbertVis
ChIPseqR
updated 14 months ago by
James W. MacDonald
68k • written 14 months ago by
chase.mateusiak
• 0
0
votes
2
replies
585
views
Downloading Metagenomic Data with Higher Taxonomic Units
curatedMetagenomicData
updated 14 months ago by
Levi Waldron
★ 1.1k • written 15 months ago by
ua51601
• 0
46,723 results • Page
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Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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by
Gordon Smyth
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I updated the above answer today.
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I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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@gordonsmyth Noted, thank you very much.
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