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Votes
0
votes
5
replies
1.7k
views
GenomicInteractions duplicate annotations
duplicate
GenomicInteractions
5.7 years ago
dogancan
• 0
4
votes
6
replies
5.7k
views
linear mixed models using edgeR+limma
linear mixed model
edger
limma
voom
RNA-seq
updated 5.7 years ago by
Gordon Smyth
53k • written 5.7 years ago by
weichengz
▴ 10
2
votes
2
replies
1.9k
views
How to access metadata of GAlignments objects
rtracklayer
Rsamtools
GAlignments
GRanges
metadata
updated 5.7 years ago by
Hervé Pagès
16k • written 5.7 years ago by
Robert
▴ 10
0
votes
1
reply
8.3k
views
How to make PCA plot using DESeq2 for a group design
deseq2
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
Jitendra
▴ 10
4
votes
10
replies
4.6k
views
how to analyze WGCNA results?
cancer
probe
deseq2
annotation
normalization
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
rajpal22288
▴ 10
6
votes
7
replies
4.0k
views
edgeR + tximport: calcNormFactors and the usage of offsets
edgeR
tximport
differential expression
updated 12 months ago by
Gordon Smyth
53k • written 5.7 years ago by
hollandademello
▴ 20
0
votes
5
replies
2.3k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
rita.monteiro
• 0
2
votes
3
replies
2.2k
views
DESeq2 LRT test for multi-factor designs
deseq2
updated 3.8 years ago by
Michael Love
43k • written 5.7 years ago by
mep19
• 0
3
votes
6
replies
1.9k
views
Better way to find head to head GRanges?
promoter
updated 5.7 years ago by
Hervé Pagès
16k • written 5.7 years ago by
Charles Plessy
▴ 180
1
vote
4
replies
1.4k
views
CAGEr quantilePositions() takes forever to run
CAGEr
quantilePositions
5.7 years ago
mirkocelii
▴ 40
0
votes
1
reply
950
views
DESeq2 for normalizing metagenomic counts
deseq2
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
ajgasparrini
• 0
0
votes
1
reply
538
views
plot function in flowType under R4.0.0
software error
5.7 years ago
lifengt
• 0
0
votes
2
replies
629
views
How to find differential gene and expression analysis using DESeq or edgeR
edger
deseq2
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
sekhwal
• 0
0
votes
2
replies
671
views
about function parameters
software error
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
1006920318
• 0
1
vote
8
replies
4.2k
views
How to change XLOC ID to Gene symbol from Cuffdiff ?
RNA-seq / XLOC
cuffdiff
updated 4.0 years ago by
Lan
• 0 • written 5.7 years ago by
mg.mahabad1365
• 0
0
votes
4
replies
2.0k
views
Error attaching TIN
software error
GO.db
TIN
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
AB3
• 0
1
vote
1
reply
797
views
Meeting Questions when using Deseq2paper package
deseq2
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
zhangdy1996
• 0
0
votes
0
replies
1.1k
views
How to overlap heatmaps on Gviz?
Givz
heatmap
overlap
combine information
5.7 years ago
kris.petrini
• 0
0
votes
1
reply
2.3k
views
Error while installing GSVA
software error
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
SE
▴ 10
2
votes
7
replies
1.2k
views
lfcShrink giving error
deseq2
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
angkoo
▴ 10
0
votes
1
reply
1.4k
views
error when forging a BSgenome
BSgenome
updated 5.7 years ago by
shepherl
4.3k • written 5.7 years ago by
Didi
▴ 10
4
votes
7
replies
6.2k
views
Analyzing TCGA RSEM Data with DESeq2 downloaded from FireBrowse
deseq2
tximport
tcga
rsem
firebrowse
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
J. Smith
• 0
0
votes
4
replies
2.1k
views
scran's quickCluster error
scran
updated 5.7 years ago by
Aaron Lun
★ 29k • written 5.7 years ago by
marc.tormo
• 0
0
votes
0
replies
1.4k
views
ChIPseeker error when I wnat to get tagMatrix
Chipseeker
TxDb
getpromoters
software error
5.7 years ago
hfyuan2016
• 0
0
votes
8
replies
1.7k
views
To start organising data for DESeq2
deseq2
updated 5.7 years ago by
swbarnes2
★ 1.4k • written 5.7 years ago by
angkoo
▴ 10
0
votes
9
replies
2.8k
views
i can't install metade package
software error
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
1006920318
• 0
23
votes
11
replies
3.0k
views
Bioconductor vs BioConductor
project
updated 5.7 years ago by
Gordon Smyth
53k • written 5.7 years ago by
Jim Hester
▴ 40
1
vote
7
replies
3.3k
views
tximport from RSEM expected counts: is it possible to import from a table rather than a file?
tximport
limma
rnaseq
updated 4.8 years ago by
Aubrey
• 0 • written 5.7 years ago by
Ahdee
▴ 60
0
votes
2
replies
1.1k
views
Extraction of individual results from DESeq2 data
deseq2
updated 5.7 years ago by
swbarnes2
★ 1.4k • written 5.7 years ago by
martin.busch
• 0
0
votes
1
reply
556
views
Server disk full for archived biomaRt database
software error
updated 5.7 years ago by
James W. MacDonald
68k • written 5.7 years ago by
g.hemani
• 0
1
vote
5
replies
4.1k
views
Updating Out of Date BiocManager Packages
biocmanager
valid
update
packages
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
bs14ab
• 0
1
vote
1
reply
737
views
RMarkdown in combination with OUTRIDER
software error
updated 3.0 years ago by
Christian Mertes
• 0 • written 5.7 years ago by
m.plandsoen
▴ 10
0
votes
1
reply
1.1k
views
Are the ordering of outputs of methylation matrix and coordinates from predictedMeth() the same?
biseq
R
methylation
5.7 years ago
AishaD
• 0
1
vote
1
reply
776
views
correct use of regularized log/VST values from deseq2
deseq2
updated 5.7 years ago by
Michael Love
43k • written 5.7 years ago by
mtswanson2017
• 0
1
vote
7
replies
4.0k
views
High padj in DESeq2
deseq2
RNA-seq
microRNA
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
saulwang0102
▴ 10
2
votes
6
replies
2.1k
views
Nested design matrix in edgeR
edger
limma
paired
blocking
ruvseq
updated 5.7 years ago by
Gordon Smyth
53k • written 5.7 years ago by
ScA
• 0
0
votes
0
replies
1.1k
views
Subset samples expressing genes for DEXSeq or DRIMSeq analysis
DEXSeq
DRIMSeq
5.7 years ago
alexis.weinreb
• 0
0
votes
0
replies
969
views
Correcting for multiple comparisons in permutation procedure using multtest
multtest
ss.maxT
ss.minP
sd.maxT
5.7 years ago
john.gordon.yellow
• 0
0
votes
0
replies
1.4k
views
listSRAfile: Error in if (is.na(sra_acc$run[i])) { : argument is of length zero
SRAdb
5.7 years ago
Aditya
▴ 160
0
votes
4
replies
1.4k
views
ProFIA package error for noise estimation
software error
proFIA
HRMS
FIA
Metabolomics
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
Esther G.
• 0
0
votes
1
reply
538
views
How to design block vector for duplicateCorrelation()
limma
updated 5.7 years ago by
Gordon Smyth
53k • written 5.7 years ago by
gulusunshine
• 0
2
votes
4
replies
1.6k
views
MakeOrgPackageFromNCBI SQL error
MakeOrgPackageFromNCBI
NCBI
SQL
AnnotationForge
updated 5.7 years ago by
James W. MacDonald
68k • written 5.7 years ago by
chefer
• 0
1
vote
6
replies
2.0k
views
Behaviour of getCTSS on a CAGEset - extra reads?
cager
cage
ctss
updated 5.7 years ago by
Charles Plessy
▴ 180 • written 6.5 years ago by
sarac
▴ 20
0
votes
2
replies
1.6k
views
How to create GRanges for TES
GenomicFeatures
TxDb
CLIP-Seq
updated 5.7 years ago by
Michael Lawrence
★ 11k • written 5.7 years ago by
mar.pieraccioli
▴ 10
0
votes
3
replies
2.0k
views
PureCN gene LOH very common, amp/del not
PureCN
gene
amplification
deletion
loh
updated 5.7 years ago by
markus.riester
▴ 130 • written 5.7 years ago by
twtoal
▴ 10
3
votes
4
replies
1.3k
views
Correct input data for avereps function (for averaging multiple probes for same gene)
limma
updated 5.7 years ago by
James W. MacDonald
68k • written 5.7 years ago by
Naren C S
• 0
5
votes
2
replies
3.0k
views
How to extract positions present in one genomic ranges object and not the other?
genomicranges
r
overlap
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
Grinch
• 0
1
vote
5
replies
3.5k
views
Peer's Certificate issuer is not recognized
BioMart
updated 5.7 years ago by
Mike Smith
★ 6.6k • written 5.7 years ago by
ilysR
• 0
0
votes
2
replies
1.6k
views
Gviz AlignmentsTrack: how to prevent reads from overlapping each other
Gviz
updated 5.7 years ago by
Robert Ivanek
▴ 750 • written 5.7 years ago by
ari.loytynoja
• 0
0
votes
5
replies
1.8k
views
Error with DESeqDataSetFromHTSeqCount
DESeqDataSetFromHTSeqCount
updated 5.7 years ago by
Kevin Blighe
★ 4.0k • written 5.7 years ago by
tjk30
• 0
46,726 results • Page
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
• 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
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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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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