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450k
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0
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views
cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
19 months ago
edward.esiribloom
• 0
3
votes
6
replies
2.0k
views
Minfi can't combineArrays
RGset
combinearrays
450k
minfi
updated 3.2 years ago by
James W. MacDonald
67k • written 3.2 years ago by
Sophie Marion de Proce
• 0
0
votes
0
replies
864
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
4.8 years ago
A
▴ 40
6
votes
3
replies
11k
views
Minfi issue: return code from pthread_create() is 22
minfi
450k
updated 20 months ago by
Sin
• 0 • written 5.3 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 5.2 years ago by
James W. MacDonald
67k • written 5.2 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 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
antgomo
• 0
1
vote
6
replies
2.3k
views
Reading 450k data in minfi
450K
minfi
updated 5.7 years ago by
laurenz.holcik
• 0 • written 5.7 years ago by
lalchungnungabt17
• 0
0
votes
3
replies
1.6k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K
CSV
normalization
minfi
ChAMP
updated 6.4 years ago by
Yuan Tian
▴ 290 • written 6.4 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
6.7 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
7.1 years ago
david.ch
• 0
0
votes
0
replies
1.5k
views
minfi estimateCellCounts normalized beta values adjusted for cell type
minfi
450k
7.4 years ago
igor
▴ 50
6
votes
2
replies
4.7k
views
Plotting Differentially Methylated Regions
minfi
bumphunter
450k
region
updated 7.9 years ago by
Dimitris Polychronopoulos
▴ 80 • written 8.6 years ago by
cardenasca
▴ 40
0
votes
2
replies
2.3k
views
Error using Bumphunter and Block finder using CHAMP
champ
methylation
450k
7.9 years ago
hrishi27n
▴ 20
0
votes
0
replies
1.2k
views
Error in assay colnames when using readGEORawFile function in "minfi" package
minfi
methylation
450k
7.9 years ago
moonkinwen
• 0
2
votes
1
reply
1.8k
views
Minfi: estimateCellCounts rgSet
minfi
450k
flowsorted.blood.450k
updated 7.9 years ago by
Habil Zare
▴ 200 • written 8.6 years ago by
cardenasca
▴ 40
0
votes
0
replies
1.6k
views
News:
ChAMP2 is online
epigenetics
EPIC
450K
ChAMP
News
8.1 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
8.2 years ago
Yuan Tian
▴ 90
3
votes
3
replies
3.5k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
8.6 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 8.6 years ago by
James W. MacDonald
67k • written 8.7 years ago by
AST
▴ 60
4
votes
10
replies
4.8k
views
Illumina MethylationEPIC vs. 450K
methylumi
minfi
illuminahumanmethylation450k.db
450k
methyanalysis
updated 8.7 years ago by
Peter Hickey
▴ 740 • written 8.7 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
8.7 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 • updated 8.7 years ago
Pablo marin-garcia
▴ 90
0
votes
0
replies
1.5k
views
Repetitive motifs on Illumina 450k derived sequences
illumina
450k
motifs
meme
8.8 years ago
Gustavo Fernández Bayón
▴ 440
0
votes
6
replies
6.6k
views
ComBat with multiple batches
sva
combat
450k
8.8 years ago
ben.run974
• 0
0
votes
4
replies
2.7k
views
preprocessFunnorm in minfi
minfi
450k
illuminahumanmethylation450k.db
normalization
updated 8.9 years ago by
James W. MacDonald
67k • written 8.9 years ago by
b.tawk
• 0
1
vote
7
replies
3.8k
views
Loading beta values into minfi
minfi
450k
updated 9.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.0 years ago by
CC
▴ 10
0
votes
2
replies
2.0k
views
Loading RData files into ChAMP
microarray
champ
450k
updated 9.1 years ago by
champ450k
• 0 • written 9.1 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
9.2 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 9.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.3 years ago by
metamaden
▴ 10
6
votes
3
replies
3.4k
views
Limma on Methylation Data - Fold Change Question
limma
450k
updated 9.3 years ago by
Aaron Lun
★ 28k • written 9.3 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
9.5 years ago
Aileen Bahl
▴ 10
0
votes
1
reply
4.4k
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 9.7 years ago by
belinda.phipson
▴ 40 • written 9.7 years ago by
Ed Schwalbe
▴ 10
33 results • Page
1 of 1
Recent ...
Replies
Answer: single cell RNA seq pseudobulk batch correction
by
James W. MacDonald
67k
You can exclude the females from the non-responders.
Answer: Normalized counts to be used in decoupleR from deseq2 results
by
James W. MacDonald
67k
No, you never use normalized counts for anything but plotting. Can you point out the example that uses normalized counts?
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
If you care to know more about the process, there is a [GitHub with all the code][1]. It's pretty complicated though - the readme alone is …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
Guido Hooiveld
★ 4.1k
Thanks; I did not know which file exactly is being used. Good catch regarding the discrepancy between the 2 web pages. I will get in touch …
Answer: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
by
James W. MacDonald
67k
The data for the `OrgDb` packages comes directly from NCBI, and in this case the symbols come from the gene_info.gz file you [can get from …
Votes
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: Extension to knitr/Rmarkdown to ignore only specific warnings (not all) in a chu
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
Comment: limma technical repeat correction
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