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minfi
•
reset
0
votes
0
replies
80
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
11 days ago
Felix
• 0
0
votes
1
reply
125
views
Matrix multiplication error to estimate telomere length
methylclockData
minfi
methylclock
minfidata
updated 19 days ago by
James W. MacDonald
65k • written 20 days ago by
sharangiiv
• 0
0
votes
7
replies
337
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 4 weeks ago by
James W. MacDonald
65k • written 4 weeks ago by
sharangiiv
• 0
0
votes
2
replies
285
views
EPIC array hg38 annotation?
minfi
DMRcate
5 weeks ago
mycetes
• 0
0
votes
0
replies
192
views
Normalization in methylation analysis
Methylation
minfi
preprocessQuantile
MethylationArrayData
preprocessFunnorm
3 months ago
kyj2226
• 0
3
votes
2
replies
388
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE
CpG
minfi
CpGinterrogation
3 months ago
kyj2226
• 0
1
vote
5
replies
923
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 14 days ago by
James W. MacDonald
65k • written 3 months ago by
rae.alshammari
▴ 10
0
votes
1
reply
238
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 3 months ago by
Basti
▴ 750 • written 3 months ago by
Ana
• 0
0
votes
5
replies
798
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
5 months ago
dorota.komar
• 0
0
votes
2
replies
553
views
minfi differential methylation analysis errors
minfi
5 months ago
matthew.sinton
• 0
0
votes
3
replies
466
views
minfi bumphunter - probe IDs
minfi
bumphunter
updated 5 months ago by
Basti
▴ 750 • written 5 months ago by
dorota.komar
• 0
0
votes
14
replies
1.5k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 7 weeks ago by
nguyen
• 0 • written 6 months ago by
Deepa
• 0
0
votes
1
reply
338
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC
minfi
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
phelankj
• 0
0
votes
3
replies
816
views
Batch correction using control probes in EPIC array data
RnBeads
minfiData
minfi
EPICarray
updated 10 months ago by
Basti
▴ 750 • written 10 months ago by
Jitendra
▴ 10
0
votes
1
reply
483
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 10 months ago by
Basti
▴ 750 • written 10 months ago by
Saanchi
• 0
0
votes
1
reply
485
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis
minfi
MethylationArrayData
minfiDataEPIC
MethylationArray
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
Grace
• 0
0
votes
0
replies
375
views
cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
12 months ago
edward.esiribloom
• 0
4
votes
5
replies
5.1k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0
minfi
updated 4 months ago by
jay
• 0 • written 12 months ago by
luca.s
▴ 50
0
votes
1
reply
544
views
specifying comparison of interest in the minfi Bumhunter function
limma
bumphunter
methylationArrayAnalysis
minfi
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
edward.esiribloom
• 0
0
votes
4
replies
923
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
Grace
• 0
1
vote
3
replies
735
views
Analysing Genome Studio .txt files with minfi
minfi
updated 12 months ago by
James W. MacDonald
65k • written 12 months ago by
alyena
• 0
0
votes
5
replies
1.1k
views
minfi error read.metharray.exp
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
written 12 months ago by
Grace
• 0
0
votes
1
reply
614
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic
read.metharray.sheet
list.files
minfi
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
Diogenesis
• 0
2
votes
3
replies
846
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 14 months ago by
belinda.phipson
▴ 40 • written 14 months ago by
Lukas
• 0
0
votes
1
reply
897
views
minfi read.metharray.sheet error
minfi
updated 15 months ago by
James W. MacDonald
65k • written 15 months ago by
jasmine_chappell
• 0
0
votes
1
reply
849
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile
noob
Normalization
minfi
minfiDataEPIC
updated 19 months ago by
James W. MacDonald
65k • written 19 months ago by
mikat
• 0
0
votes
0
replies
492
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
19 months ago
calen.p.ryan
• 0
0
votes
0
replies
665
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter
minfi
genomi
21 months ago
runye
• 0
0
votes
1
reply
820
views
what is the format of DMPfinder in minfi package
minfi
updated 21 months ago by
Basti
▴ 750 • written 22 months ago by
Fateme
• 0
0
votes
3
replies
1.1k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
23 months ago • updated 22 months ago
ramonfallon
▴ 20
0
votes
2
replies
2.6k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 23 months ago by
Will
• 0 • written 8.5 years ago by
metamaden
▴ 10
0
votes
0
replies
840
views
Annotation Illumina Infinium Mouse Methylation
Illumina
minfi
IlluminaHumanMethylationEPICmanifest
23 months ago
octaviompa
• 0
0
votes
0
replies
610
views
Minfi package: controlStripPlot colors
minfi
2.1 years ago
Rebecca
• 0
0
votes
1
reply
778
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
failingprobes
detectionP
minfi
updated 2.1 years ago by
James W. MacDonald
65k • written 2.1 years ago by
Lilly
• 0
0
votes
9
replies
3.0k
views
clarification about bumphunter value output
minfi
bumphunter
updated 9 months ago by
Jennifer Dehner
• 0 • written 6.0 years ago by
src3
• 0
0
votes
1
reply
840
views
EPIC ARRAY ANALYSIS
minfiDataEPIC
#SexPrediction
minfi
updated 2.5 years ago by
Basti
▴ 750 • written 2.5 years ago by
nucasa
• 0
0
votes
0
replies
687
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi
minfiData
MethylationArrayData
2.6 years ago
ponche_de_kiwi
• 0
3
votes
6
replies
1.6k
views
Minfi can't combineArrays
RGset
combinearrays
450k
minfi
updated 2.6 years ago by
James W. MacDonald
65k • written 2.6 years ago by
Sophie Marion de Proce
• 0
0
votes
0
replies
725
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi
limma
lmm
lmfit
dmpFinder
2.8 years ago
kyleyxw
• 0
2
votes
2
replies
812
views
How to overcome issue linked to loading big R object
minfi
R
methylation
2.9 years ago
Federica
▴ 10
0
votes
0
replies
744
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl
minfi
2.9 years ago
Jeff
▴ 20
0
votes
1
reply
1.3k
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest
minfi
conumee
updated 2.9 years ago by
volker hovestadt
▴ 40 • written 2.9 years ago by
theresa.walder
• 0
1
vote
8
replies
1.3k
views
EPIC array single replicate pipeline?
minfi
methylationArrayAnalysis
3.0 years ago • updated 2.9 years ago
chay
• 0
0
votes
1
reply
1.9k
views
plotSex error message
minfiData
plotsex
minfi
minfiDataEPIC
r
updated 3.1 years ago by
suman
• 0 • written 3.1 years ago by
Bethan
• 0
1
vote
4
replies
2.5k
views
Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData
methy
Bioconductor
minfi
3.1 years ago
shweta
• 0
1
vote
5
replies
3.9k
views
minfi - error when reading idat files
minfi
methylation
updated 18 months ago by
Sajad Wani
• 0 • written 6.7 years ago by
stewart999
▴ 10
0
votes
9
replies
2.6k
views
Rhdf5lib installation problem
minfi
Rhdf5lib
updated 3.2 years ago by
Mike Smith
★ 6.4k • written 3.2 years ago by
Giovanni Calice
▴ 160
0
votes
2
replies
1.6k
views
Beyond dmpFinder for methylation analysis, using limma for covariates
minfiDataEPIC
arrays
limma
minfi
Epigenetics
updated 3.3 years ago by
Gordon Smyth
50k • written 3.3 years ago by
Jeff
▴ 20
0
votes
6
replies
1.4k
views
NaN values in beta/M values matrices of RGChannelSet are imputed during normalization?
minfiData
methylationArrayAnalysis
MethylationArrayData
minfi
updated 3.3 years ago by
Kasper Daniel Hansen
★ 6.5k • written 3.4 years ago by
omorante
• 0
0
votes
2
replies
989
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi
minfi
microarray
epic
3.9 years ago • updated 3.4 years ago
Nala
• 0
50 results • Page
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Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
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Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: padj-based gradient scale from barplot (clusterProfiler results) does not work p
C: How to check that the reads in two fastq files are in the same order
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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