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450k
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0
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576
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cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
20 months ago
edward.esiribloom
• 0
3
votes
6
replies
2.1k
views
Minfi can't combineArrays
RGset
combinearrays
450k
minfi
updated 3.3 years ago by
James W. MacDonald
67k • written 3.3 years ago by
Sophie Marion de Proce
• 0
0
votes
0
replies
884
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
4.9 years ago
A
▴ 40
6
votes
3
replies
11k
views
Minfi issue: return code from pthread_create() is 22
minfi
450k
updated 21 months ago by
Sin
• 0 • written 5.4 years ago by
jshouse
▴ 10
0
votes
1
reply
2.2k
views
How to analyse 450k and EPIC methylation data together?
minfi
450k
EPIC
analysis
updated 5.3 years ago by
James W. MacDonald
67k • written 5.3 years ago by
maduran
• 0
0
votes
3
replies
1.4k
views
Limma for cell components effect on response
450k
EPIC
minfi
limma
cell components
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
antgomo
• 0
1
vote
6
replies
2.4k
views
Reading 450k data in minfi
450K
minfi
updated 5.7 years ago by
laurenz.holcik
• 0 • written 5.8 years ago by
lalchungnungabt17
• 0
0
votes
3
replies
1.7k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K
CSV
normalization
minfi
ChAMP
updated 6.5 years ago by
Yuan Tian
▴ 290 • written 6.5 years ago by
Simone
▴ 190
0
votes
0
replies
1.2k
views
how to analyze "Beta-score" and get CNVdata using Comunee
conumee
CNV
450K
6.8 years ago
bird.of.clockwise
• 0
0
votes
0
replies
1.4k
views
Error when using Champ.SVD() function
champ
champs.svd()
450K
illimina 450k methylation
champ 2.8.9
7.2 years ago
david.ch
• 0
0
votes
0
replies
1.5k
views
minfi estimateCellCounts normalized beta values adjusted for cell type
minfi
450k
7.5 years ago
igor
▴ 50
6
votes
2
replies
4.7k
views
Plotting Differentially Methylated Regions
minfi
bumphunter
450k
region
updated 8.0 years ago by
Dimitris Polychronopoulos
▴ 80 • written 8.7 years ago by
cardenasca
▴ 40
0
votes
2
replies
2.3k
views
Error using Bumphunter and Block finder using CHAMP
champ
methylation
450k
8.0 years ago
hrishi27n
▴ 20
0
votes
0
replies
1.3k
views
Error in assay colnames when using readGEORawFile function in "minfi" package
minfi
methylation
450k
8.0 years ago
moonkinwen
• 0
2
votes
1
reply
1.8k
views
Minfi: estimateCellCounts rgSet
minfi
450k
flowsorted.blood.450k
updated 8.0 years ago by
Habil Zare
▴ 200 • written 8.7 years ago by
cardenasca
▴ 40
0
votes
0
replies
1.6k
views
News:
ChAMP2 is online
epigenetics
EPIC
450K
ChAMP
News
8.2 years ago
Yuan Tian
▴ 90
0
votes
1
reply
2.2k
views
News:
Bug in ChAMP package champ.SVD() function
champ
methylation
450k
SVD
EPIC
News
8.3 years ago
Yuan Tian
▴ 90
3
votes
3
replies
3.5k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.7 years ago
AST
▴ 60
4
votes
4
replies
3.4k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 8.7 years ago by
James W. MacDonald
67k • written 8.7 years ago by
AST
▴ 60
4
votes
10
replies
4.9k
views
Illumina MethylationEPIC vs. 450K
methylumi
minfi
illuminahumanmethylation450k.db
450k
methyanalysis
updated 8.8 years ago by
Peter Hickey
▴ 740 • written 8.8 years ago by
Ahdee
▴ 50
0
votes
0
replies
1.6k
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina
450k
ChAMP
paired test
8.8 years ago
walter_teng
• 0
3
votes
1
reply
1.4k
views
two 450K methylation array manifests. where is the difference?
methylation
450k
8.8 years ago
Pablo marin-garcia
▴ 90
0
votes
0
replies
1.5k
views
Repetitive motifs on Illumina 450k derived sequences
illumina
450k
motifs
meme
8.9 years ago
Gustavo Fernández Bayón
▴ 440
0
votes
6
replies
6.7k
views
ComBat with multiple batches
sva
combat
450k
8.9 years ago
ben.run974
• 0
0
votes
4
replies
2.7k
views
preprocessFunnorm in minfi
minfi
450k
illuminahumanmethylation450k.db
normalization
updated 9.0 years ago by
James W. MacDonald
67k • written 9.0 years ago by
b.tawk
• 0
1
vote
7
replies
3.9k
views
Loading beta values into minfi
minfi
450k
updated 9.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.1 years ago by
CC
▴ 10
0
votes
2
replies
2.0k
views
Loading RData files into ChAMP
microarray
champ
450k
updated 9.2 years ago by
champ450k
• 0 • written 9.2 years ago by
CC
▴ 10
0
votes
0
replies
1.5k
views
minfi v1.14 through champ: read.450k error with file path name
minfi
champ
illumina
450k
9.3 years ago
jeroen
• 0
1
vote
2
replies
2.0k
views
QC/normalization standards for cancer studies with 450k array data
minfi
watermelon
cancer
450k
normalization
updated 9.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.4 years ago by
metamaden
▴ 10
6
votes
3
replies
3.4k
views
Limma on Methylation Data - Fold Change Question
limma
450k
updated 9.4 years ago by
Aaron Lun
★ 28k • written 9.4 years ago by
andrew.j.skelton73
▴ 370
0
votes
4
replies
1.9k
views
Use of confounders in downstream analysis
limma
GSA
confounding
within-pair analysis
450k
9.6 years ago
Aileen Bahl
▴ 10
0
votes
1
reply
4.5k
views
methyAnalysis M values and Beta Values
methyAnalysis
methyanalysis
450k
updated 9.7 years ago by
Pan Du
▴ 80 • written 9.7 years ago by
andrew.j.skelton73
▴ 370
1
vote
2
replies
2.5k
views
Bias correction for enrichment analysis of 450k methylation data => feed bias adjusted genes into IPA
goseq
450k
enrichment
updated 9.8 years ago by
belinda.phipson
▴ 40 • written 9.8 years ago by
Ed Schwalbe
▴ 10
33 results • Page
1 of 1
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Replies
Comment: Differential Expression Genes as Independent Variables
by
Dario Strbenac
★ 1.5k
Also, the reason why gene abundance is the dependent variable and is iterated over is that there are far more genes than there are samples …
Comment: rrvgo::calculateSimMatrix() error
by
Phila
• 0
Thanks for sharing the solution. It helps me. [nced cloud][1] [1]: https://my-ncedcloud-login.us/
Comment: Merge Replicates vs Mixed Model
by
gabriel.hoffman
▴ 170
For your proteomics data, your normalization is correct. I had assumed it was RNA-seq because that is what I think about most. When using…
Comment: What type of counts data to import for performing Isoform analysis in edgeR
by
mohammedtoufiq91
▴ 10
@gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you.
Comment: Differential Expression Genes as Independent Variables
by
Gordon Smyth
52k
Such an analysis cannot be done in limma. Sorry, I cannot tell you how to do it or even whether it is possible.
Votes
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
Transcript-level differential expression using DESeq2
Comment: What type of counts data to import for performing Isoform analysis in edgeR
Answer: What type of counts data to import for performing Isoform analysis in edgeR
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