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qsea
•
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0
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306
views
Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
11 months ago
User3088
• 0
0
votes
1
reply
682
views
QSEA:Error in h(simpleError(msg, call))
qsea
16 months ago
kf
• 0
1
vote
2
replies
701
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 20 months ago by
Researcher
▴ 10
0
votes
2
replies
807
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
23 months ago • updated 11 months ago
User3088
• 0
9
votes
18
replies
4.9k
views
Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
illimina 450k methylation
qsea
MEDIPS
TCGA
updated 2.0 years ago by
Matthias Lienhard
▴ 280 • written 8.8 years ago by
justinburgener
▴ 20
2
votes
1
reply
947
views
QSEA: normalisation >> sequencing preference
qsea
updated 2.9 years ago by
Matthias Lienhard
▴ 280 • written 2.9 years ago by
a.riediger
▴ 20
1
vote
1
reply
1.4k
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 2.9 years ago by
Matthias Lienhard
▴ 280 • written 2.9 years ago by
a.riediger
▴ 20
1
vote
4
replies
2.0k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM
edgeR
qsea
MEDIPS
updated 3.3 years ago by
Simon Pearce
• 0 • written 3.3 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.4k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 3.4 years ago by
Simon Pearce
• 0 • written 3.5 years ago by
Marianna
▴ 20
3
votes
8
replies
2.2k
views
Annotation using QSEA package
DNAMethylation
QSEA
MEDIP
4.6 years ago
rtrivedi1
▴ 10
7
votes
9
replies
2.8k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
4.7 years ago • updated 4.6 years ago
rtrivedi1
▴ 10
0
votes
1
reply
1.1k
views
No beta scores generated in samples eluted at low salt concentration (MBD-seq) which aims to capture low methylated fragments?
qsea
updated 4.7 years ago by
Matthias Lienhard
▴ 280 • written 4.8 years ago by
el466
• 0
1
vote
1
reply
1.5k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 5.0 years ago by
Matthias Lienhard
▴ 280 • written 5.0 years ago by
mbk0asis
• 0
0
votes
2
replies
1.2k
views
Qsea - plotCoverage
Qsea
updated 5.7 years ago by
Matthias Lienhard
▴ 280 • written 5.7 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.6k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 5.9 years ago by
Matthias Lienhard
▴ 280 • written 5.9 years ago by
Simon Pearce
• 0
0
votes
1
reply
1.1k
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 5.9 years ago by
Matthias Lienhard
▴ 280 • written 5.9 years ago by
gaurav4thareja
▴ 20
1
vote
4
replies
2.3k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 12 months ago by
Lukas
▴ 20 • written 6.4 years ago by
LNathanson
• 0
0
votes
0
replies
1.5k
views
Indexing large chromosomes (like wheat) bam files in Rsamtools
Rsamtools
QSEA
MEDIPS
7.3 years ago
saripalligautam86
▴ 10
0
votes
1
reply
1.2k
views
Error running the addCoverage command in QSEA with a custom BSGenome reference
qsea
updated 7.6 years ago by
Matthias Lienhard
▴ 280 • written 7.6 years ago by
apt.university
• 0
0
votes
8
replies
2.3k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 7.7 years ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
wildist
• 0
0
votes
3
replies
1.7k
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 7.9 years ago by
Matthias Lienhard
▴ 280 • written 7.9 years ago by
geekyvt
• 0
1
vote
2
replies
1.4k
views
QSEA: Error while addLibraryFactors
QSEA
updated 7.9 years ago by
Matthias Lienhard
▴ 280 • written 7.9 years ago by
geekyvt
• 0
1
vote
3
replies
1.8k
views
QSEA Error while loading the bam files
qsea
updated 7.9 years ago by
Matthias Lienhard
▴ 280 • written 7.9 years ago by
geekyvt
• 0
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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
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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
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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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