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450K
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cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
2.0 years ago
edward.esiribloom
• 0
3
votes
6
replies
2.3k
views
Minfi can't combineArrays
RGset
combinearrays
450k
minfi
updated 3.7 years ago by
James W. MacDonald
68k • written 3.7 years ago by
Sophie Marion de Proce
• 0
0
votes
0
replies
954
views
Error when trying to read in idat files in methylumi
methylumi
450k
methylation
methylome
5.2 years ago
A
▴ 60
6
votes
3
replies
12k
views
Minfi issue: return code from pthread_create() is 22
minfi
450k
updated 2.1 years ago by
Sin
• 0 • written 5.7 years ago by
jshouse
▴ 10
0
votes
1
reply
2.5k
views
How to analyse 450k and EPIC methylation data together?
minfi
450k
EPIC
analysis
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
maduran
• 0
0
votes
3
replies
1.5k
views
Limma for cell components effect on response
450k
EPIC
minfi
limma
cell components
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
antgomo
• 0
1
vote
6
replies
2.6k
views
Reading 450k data in minfi
450K
minfi
updated 6.1 years ago by
laurenz.holcik
• 0 • written 6.1 years ago by
lalchungnungabt17
• 0
0
votes
3
replies
1.8k
views
QC and normalization of 450K data from CSVs instead of IDATs
450K
CSV
normalization
minfi
ChAMP
updated 6.8 years ago by
Yuan Tian
▴ 290 • written 6.8 years ago by
Simone
▴ 190
0
votes
0
replies
1.3k
views
how to analyze "Beta-score" and get CNVdata using Comunee
conumee
CNV
450K
7.1 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
7.5 years ago
david.ch
• 0
0
votes
0
replies
1.6k
views
minfi estimateCellCounts normalized beta values adjusted for cell type
minfi
450k
7.8 years ago
igor
▴ 50
6
votes
2
replies
5.1k
views
Plotting Differentially Methylated Regions
minfi
bumphunter
450k
region
updated 8.3 years ago by
Dimitris Polychronopoulos
▴ 80 • written 9.1 years ago by
cardenasca
▴ 40
0
votes
2
replies
2.5k
views
Error using Bumphunter and Block finder using CHAMP
champ
methylation
450k
8.4 years ago • updated 8.3 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
8.3 years ago
moonkinwen
• 0
2
votes
1
reply
1.9k
views
Minfi: estimateCellCounts rgSet
minfi
450k
flowsorted.blood.450k
updated 8.4 years ago by
Habil Zare
▴ 200 • written 9.0 years ago by
cardenasca
▴ 40
0
votes
0
replies
1.7k
views
News:
ChAMP2 is online
epigenetics
EPIC
450K
ChAMP
News
8.5 years ago
Yuan Tian
▴ 90
0
votes
1
reply
2.4k
views
News:
Bug in ChAMP package champ.SVD() function
champ
methylation
450k
SVD
EPIC
News
8.6 years ago
Yuan Tian
▴ 90
3
votes
3
replies
3.7k
views
Adjustment of covariates in 450k data using Limma
limma
covariates
450k
9.0 years ago
AST
▴ 60
4
votes
4
replies
3.6k
views
How to remove unwanted probes before normalization in 450k data
minfi
450k
champ
rnbeads
updated 9.0 years ago by
James W. MacDonald
68k • written 9.1 years ago by
AST
▴ 60
4
votes
10
replies
5.2k
views
Illumina MethylationEPIC vs. 450K
methylumi
minfi
illuminahumanmethylation450k.db
450k
methyanalysis
updated 9.1 years ago by
Peter Hickey
▴ 750 • written 9.1 years ago by
Ahdee
▴ 60
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
9.1 years ago
walter_teng
• 0
3
votes
1
reply
1.5k
views
two 450K methylation array manifests. where is the difference?
methylation
450k
9.2 years ago
Pablo marin-garcia
▴ 90
0
votes
0
replies
1.5k
views
Repetitive motifs on Illumina 450k derived sequences
illumina
450k
motifs
meme
9.2 years ago
Gustavo Fernández Bayón
▴ 440
0
votes
6
replies
7.2k
views
ComBat with multiple batches
sva
combat
450k
9.2 years ago
ben.run974
• 0
0
votes
4
replies
2.9k
views
preprocessFunnorm in minfi
minfi
450k
illuminahumanmethylation450k.db
normalization
updated 9.3 years ago by
James W. MacDonald
68k • written 9.3 years ago by
b.tawk
• 0
1
vote
7
replies
4.2k
views
Loading beta values into minfi
minfi
450k
updated 9.4 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.4 years ago by
CC
▴ 10
0
votes
2
replies
2.1k
views
Loading RData files into ChAMP
microarray
champ
450k
updated 9.5 years ago by
champ450k
• 0 • written 9.5 years ago by
CC
▴ 10
0
votes
0
replies
1.6k
views
minfi v1.14 through champ: read.450k error with file path name
minfi
champ
illumina
450k
9.6 years ago
jeroen
• 0
1
vote
2
replies
2.2k
views
QC/normalization standards for cancer studies with 450k array data
minfi
watermelon
cancer
450k
normalization
updated 9.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 9.7 years ago by
metamaden
▴ 10
6
votes
3
replies
3.7k
views
Limma on Methylation Data - Fold Change Question
limma
450k
updated 9.8 years ago by
Aaron Lun
★ 28k • written 9.8 years ago by
andrew.j.skelton73
▴ 370
0
votes
4
replies
2.0k
views
Use of confounders in downstream analysis
limma
GSA
confounding
within-pair analysis
450k
10.0 years ago
Aileen Bahl
▴ 10
0
votes
1
reply
4.7k
views
methyAnalysis M values and Beta Values
methyAnalysis
methyanalysis
450k
updated 10.1 years ago by
Pan Du
▴ 80 • written 10.1 years ago by
andrew.j.skelton73
▴ 370
1
vote
2
replies
2.7k
views
Bias correction for enrichment analysis of 450k methylation data => feed bias adjusted genes into IPA
goseq
450k
enrichment
updated 10.1 years ago by
belinda.phipson
▴ 40 • written 10.1 years ago by
Ed Schwalbe
▴ 10
33 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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