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minfi
•
reset
1
vote
4
replies
195
views
minfi::read.metharray.exp
minfiData
minfi
updated 9 days ago by
Basti
▴ 780 • written 10 days ago by
clacarion
• 0
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP
DMRcate
minfi
updated 4 weeks ago by
Tim Peters
▴ 170 • written 5 months ago by
rae.alshammari
▴ 10
0
votes
4
replies
238
views
Minfi - estimatecellscount
min
minfi
updated 3 days ago by
James W. MacDonald
65k • written 4 weeks ago by
clacarion
• 0
0
votes
0
replies
186
views
Can MethylationEPIC v1 and v2 data be used together for analysis with minfi?
minfi
minfiDataEPIC
8 weeks ago
Felix
• 0
0
votes
1
reply
176
views
Matrix multiplication error to estimate telomere length
methylclockData
minfi
methylclock
minfidata
updated 9 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
sharangiiv
• 0
0
votes
7
replies
451
views
error in reading idat files and creating rgset
minfi
MethylationArray
updated 11 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
sharangiiv
• 0
0
votes
2
replies
519
views
EPIC array hg38 annotation?
minfi
DMRcate
12 weeks ago • updated 11 weeks ago
mycetes
• 0
0
votes
0
replies
253
views
Normalization in methylation analysis
Methylation
minfi
preprocessQuantile
MethylationArrayData
preprocessFunnorm
4 months ago
kyj2226
• 0
3
votes
2
replies
459
views
What is the meaning of "CpG interrogation" and "single nucleotide extension(SBE)"?
SBE
CpG
minfi
CpGinterrogation
4 months ago
kyj2226
• 0
0
votes
1
reply
314
views
Error in reading my csv file in minfi
minfiDataEPIC
minfi
updated 5 months ago by
Basti
▴ 780 • written 5 months ago by
Ana
• 0
0
votes
5
replies
915
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi
limma
6 months ago
dorota.komar
• 0
0
votes
2
replies
658
views
minfi differential methylation analysis errors
minfi
6 months ago
matthew.sinton
• 0
0
votes
3
replies
557
views
minfi bumphunter - probe IDs
minfi
bumphunter
updated 7 months ago by
Basti
▴ 780 • written 7 months ago by
dorota.komar
• 0
0
votes
14
replies
1.9k
views
Error while preprocessing raw data from methylation array using minfi package
minfi
updated 3 months ago by
nguyen
• 0 • written 8 months ago by
Deepa
• 0
0
votes
1
reply
392
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC
minfi
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
phelankj
• 0
0
votes
3
replies
931
views
Batch correction using control probes in EPIC array data
RnBeads
minfiData
minfi
EPICarray
updated 11 months ago by
Basti
▴ 780 • written 11 months ago by
Jitendra
▴ 10
0
votes
2
replies
568
views
ageData (minfi pipeline)
ageData
missMethyl
differentialvariability
minfi
updated 5 weeks ago by
CHEN
• 0 • written 11 months ago by
Saanchi
• 0
0
votes
1
reply
542
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis
minfi
MethylationArrayData
minfiDataEPIC
MethylationArray
updated 13 months ago by
Gordon Smyth
50k • written 13 months ago by
Grace
• 0
0
votes
0
replies
412
views
cpgCollapse error
450K
blockfinder
cpgCollapse
minfi
13 months ago
edward.esiribloom
• 0
4
votes
5
replies
5.9k
views
minfi support of illumina Infinium methylationEPIC v2.0
methylationEPICv2.0
minfi
updated 6 months ago by
jay
• 0 • written 13 months ago by
luca.s
▴ 50
0
votes
1
reply
606
views
specifying comparison of interest in the minfi Bumhunter function
limma
bumphunter
methylationArrayAnalysis
minfi
updated 13 months ago by
James W. MacDonald
65k • written 13 months ago by
edward.esiribloom
• 0
0
votes
4
replies
1.0k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Grace
• 0
1
vote
3
replies
826
views
Analysing Genome Studio .txt files with minfi
minfi
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
alyena
• 0
0
votes
5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis
minfiData
minfi
MethylationArrayData
MethylationArray
written 14 months ago by
Grace
• 0
0
votes
1
reply
698
views
Minfi::read.metharray.sheet, problem with pattern defined in non-local csv file
PatternLogic
read.metharray.sheet
list.files
minfi
updated 14 months ago by
James W. MacDonald
65k • written 14 months ago by
Diogenesis
• 0
2
votes
3
replies
933
views
GSEA for paired methylation data
missMethyl
GSEA
minfi
methylGSA
updated 16 months ago by
belinda.phipson
▴ 40 • written 16 months ago by
Lukas
• 0
0
votes
1
reply
991
views
minfi read.metharray.sheet error
minfi
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
jasmine_chappell
• 0
0
votes
1
reply
935
views
Density Plot using Noob Normalisation vs Quantile Normalisation
Quantile
noob
Normalization
minfi
minfiDataEPIC
updated 20 months ago by
James W. MacDonald
65k • written 20 months ago by
mikat
• 0
0
votes
0
replies
538
views
A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation
wateRmelon
Computation
minfi
21 months ago
calen.p.ryan
• 0
0
votes
0
replies
707
views
Error: 'bumphunter()' only supports matrix-backed minfi objects.
bumphunter
minfi
genomi
23 months ago
runye
• 0
0
votes
1
reply
896
views
what is the format of DMPfinder in minfi package
minfi
updated 23 months ago by
Basti
▴ 780 • written 23 months ago by
Fateme
• 0
0
votes
3
replies
1.2k
views
methylated/unmethylated media threshold (EPIC assay)
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
ChAMP
minfi
2.1 years ago • updated 23 months ago
ramonfallon
▴ 20
0
votes
2
replies
2.7k
views
Illumina 450k Manifest: Probes Mapping to Multiple RefGene Groups and Names
illuminahumanmethylation450kanno.ilmn12.hg19
minfi
illuminahumanmethylation450k.db
methylation
updated 2.0 years ago by
Will
• 0 • written 8.6 years ago by
metamaden
▴ 10
0
votes
0
replies
917
views
Annotation Illumina Infinium Mouse Methylation
Illumina
minfi
IlluminaHumanMethylationEPICmanifest
2.0 years ago
octaviompa
• 0
0
votes
0
replies
643
views
Minfi package: controlStripPlot colors
minfi
2.2 years ago
Rebecca
• 0
0
votes
1
reply
832
views
Over 800,000 probes failing to meet Detection P-value - minfi
IlluminaHumanMethylationEPICanno.ilm10b3.hg19
failingprobes
detectionP
minfi
updated 2.2 years ago by
James W. MacDonald
65k • written 2.2 years ago by
Lilly
• 0
0
votes
9
replies
3.1k
views
clarification about bumphunter value output
minfi
bumphunter
updated 11 months ago by
Jennifer Dehner
• 0 • written 6.2 years ago by
src3
• 0
0
votes
1
reply
881
views
EPIC ARRAY ANALYSIS
minfiDataEPIC
#SexPrediction
minfi
updated 2.6 years ago by
Basti
▴ 780 • written 2.6 years ago by
nucasa
• 0
0
votes
0
replies
735
views
minfi - estimateCellCounts2-proportions sum more than 1
minfi
minfiData
MethylationArrayData
2.7 years ago
ponche_de_kiwi
• 0
3
votes
6
replies
1.7k
views
Minfi can't combineArrays
RGset
combinearrays
450k
minfi
updated 2.7 years ago by
James W. MacDonald
65k • written 2.7 years ago by
Sophie Marion de Proce
• 0
0
votes
0
replies
763
views
Incorporating limma duplicateCorrelation() function into minfi dmpFinder() for a mixed model approach
minfi
limma
lmm
lmfit
dmpFinder
2.9 years ago
kyleyxw
• 0
2
votes
2
replies
870
views
How to overcome issue linked to loading big R object
minfi
R
methylation
3.0 years ago
Federica
▴ 10
0
votes
0
replies
792
views
shinyMethyl issue when using combinedArrays() from minfi - Error in object@greenControls[[i]][, o] : incorrect number of dimensions
shinyMethyl
minfi
3.1 years ago
Jeff
▴ 20
0
votes
1
reply
1.4k
views
conumee (for EPIC): query intensities not given for all probes
IlluminaHumanMethylationEPICmanifest
minfi
conumee
updated 3.0 years ago by
volker hovestadt
▴ 40 • written 3.1 years ago by
theresa.walder
• 0
1
vote
8
replies
1.4k
views
EPIC array single replicate pipeline?
minfi
methylationArrayAnalysis
3.1 years ago
chay
• 0
0
votes
1
reply
2.0k
views
plotSex error message
minfiData
plotsex
minfi
minfiDataEPIC
r
updated 3.2 years ago by
suman
• 0 • written 3.2 years ago by
Bethan
• 0
1
vote
4
replies
2.7k
views
Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData
methy
Bioconductor
minfi
3.2 years ago
shweta
• 0
1
vote
5
replies
4.1k
views
minfi - error when reading idat files
minfi
methylation
updated 19 months ago by
Sajad Wani
• 0 • written 6.8 years ago by
stewart999
▴ 10
0
votes
9
replies
2.8k
views
Rhdf5lib installation problem
minfi
Rhdf5lib
updated 3.3 years ago by
Mike Smith
★ 6.5k • written 3.3 years ago by
Giovanni Calice
▴ 160
0
votes
2
replies
1.7k
views
Beyond dmpFinder for methylation analysis, using limma for covariates
minfiDataEPIC
arrays
limma
minfi
Epigenetics
updated 3.5 years ago by
Gordon Smyth
50k • written 3.5 years ago by
Jeff
▴ 20
50 results • Page
1 of 1
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Replies
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank"
by
arfranco
▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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