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QSEA
•
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0
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320
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Batch Correction while implementing QSEA package
qsea
MEDIPS
MEDIPSData
DNAMethylation
12 months ago
User3088
• 0
0
votes
1
reply
710
views
QSEA:Error in h(simpleError(msg, call))
qsea
17 months ago
kf
• 0
1
vote
2
replies
728
views
QSEA- Extraction of Normalized methylation across the samples
qsea
ngsReports
correlation
written 21 months ago by
Researcher
▴ 10
0
votes
2
replies
837
views
Sample-specific methylation values using QSEA
DNAMethylation
cfMeDIP-seq
cfDNA
qsea
2.0 years ago • updated 12 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 2.1 years ago by
Matthias Lienhard
▴ 280 • written 8.9 years ago by
justinburgener
▴ 20
2
votes
1
reply
989
views
QSEA: normalisation >> sequencing preference
qsea
updated 3.0 years ago by
Matthias Lienhard
▴ 280 • written 3.0 years ago by
a.riediger
▴ 20
1
vote
1
reply
1.5k
views
Manual import of CNV data (created with IchorCNA) into QSEAsest wit addCNV()
ichorCNA
qsea
updated 3.0 years ago by
Matthias Lienhard
▴ 280 • written 3.0 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 3.4 years ago by
Simon Pearce
• 0 • written 3.4 years ago by
a.riediger
▴ 20
0
votes
2
replies
1.4k
views
MBD-seq non model species
MethylSeq
ramwas
MEDIPS
qsea
updated 3.5 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
4.7 years ago
rtrivedi1
▴ 10
7
votes
9
replies
2.9k
views
QSEA : Internal CNV analysis and cancer type-specific TCGA 450K Human Methylation Calibration Dataset
MEDIP-seq
CNV
TCGA450KHumanMethylationCalibrationDataset
qsea
PRAD
4.8 years ago • updated 4.7 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 4.8 years ago by
Matthias Lienhard
▴ 280 • written 4.9 years ago by
el466
• 0
1
vote
1
reply
1.5k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq
qsea
BiocParallel
updated 5.1 years ago by
Matthias Lienhard
▴ 280 • written 5.1 years ago by
mbk0asis
• 0
0
votes
2
replies
1.2k
views
Qsea - plotCoverage
Qsea
updated 5.8 years ago by
Matthias Lienhard
▴ 280 • written 5.8 years ago by
gaurav4thareja
▴ 20
1
vote
2
replies
1.7k
views
Read counts between QSEA and MEDIPs
qsea
medips
updated 6.0 years ago by
Matthias Lienhard
▴ 280 • written 6.0 years ago by
Simon Pearce
• 0
0
votes
1
reply
1.1k
views
Qsea - addEnrichmentParameters() - Using INPUT Samples
Qsea
updated 6.0 years ago by
Matthias Lienhard
▴ 280 • written 6.0 years ago by
gaurav4thareja
▴ 20
1
vote
4
replies
2.4k
views
MBDseq analysis using qsea package
qsea
MBDseq
updated 13 months ago by
Lukas
▴ 20 • written 6.5 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 7.7 years ago by
Matthias Lienhard
▴ 280 • written 7.7 years ago by
apt.university
• 0
0
votes
8
replies
2.3k
views
qsea non-TCGA 450K Human Methylation Calibration Dataset
qsea
updated 7.8 years ago by
Matthias Lienhard
▴ 280 • written 7.8 years ago by
wildist
• 0
0
votes
3
replies
1.8k
views
QSEA: Need help on creating ROI for whole genome MeDIPSeq data
qsea
updated 8.0 years ago by
Matthias Lienhard
▴ 280 • written 8.0 years ago by
geekyvt
• 0
1
vote
2
replies
1.4k
views
QSEA: Error while addLibraryFactors
QSEA
updated 8.0 years ago by
Matthias Lienhard
▴ 280 • written 8.0 years ago by
geekyvt
• 0
1
vote
3
replies
1.8k
views
QSEA Error while loading the bam files
qsea
updated 8.0 years ago by
Matthias Lienhard
▴ 280 • written 8.0 years ago by
geekyvt
• 0
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Answer: Unable to create venndiagram using VennDiagram 1.5.1 package
by
kesha
• 0
<a href=https://vavadacasinox.com/>vavadacasinox.com</a>
Comment: How to convert .raw data for use in xcms
by
a2a2asawhaa
• 0
try converting your files to the older mzXML format, which remains highly stable for XCMS. While waiting for large datasets to process, you…
Comment: Which preprocessing steps are needed before running limpa?
by
miro165sabo
• 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
by
Gordon Smyth
53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
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Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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