Showing : minfi • reset
1
vote
4
replies
195
views
minfi::read.metharray.exp
minfiData minfi
updated 9 days ago by ▴ 780 • written 10 days ago by • 0
0
votes
4
replies
238
views
Minfi - estimatecellscount
min minfi
updated 3 days ago by 65k • written 4 weeks ago by • 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 65k • written 9 weeks ago by • 0
0
votes
7
replies
451
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
0
votes
2
replies
518
views
EPIC array hg38 annotation?
minfi DMRcate
12 weeks ago • updated 11 weeks ago mycetes • 0
0
votes
0
replies
252
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
2
votes
6
replies
1.4k
views
How to get DMR for Infinium methylation EPIC v2
ChAMP DMRcate minfi
updated 4 weeks ago by ▴ 170 • written 5 months ago by ▴ 10
0
votes
1
reply
314
views
Error in reading my csv file in minfi
minfiDataEPIC minfi
updated 5 months ago by ▴ 780 • written 5 months ago by • 0
0
votes
2
replies
658
views
minfi differential methylation analysis errors
minfi
6 months ago matthew.sinton • 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
3
replies
557
views
minfi bumphunter - probe IDs
minfi bumphunter
updated 7 months ago by ▴ 780 • written 7 months ago by • 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 • 0 • written 8 months ago by • 0
0
votes
1
reply
392
views
Two EPIC Methylation Array Analysis Questions
minfiDataEPIC minfi
updated 8 months ago by 65k • written 8 months ago by • 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 ▴ 780 • written 11 months ago by ▴ 10
0
votes
2
replies
567
views
ageData (minfi pipeline)
ageData missMethyl differentialvariability minfi
updated 5 weeks ago by • 0 • written 11 months ago by • 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 50k • written 13 months ago by • 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 • 0 • written 13 months ago by ▴ 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 65k • written 13 months ago by • 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 65k • written 14 months ago by • 0
0
votes
5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 14 months ago by • 0
1
vote
3
replies
826
views
Analysing Genome Studio .txt files with minfi
minfi
updated 14 months ago by 65k • written 14 months ago by • 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 65k • written 14 months ago by • 0
2
votes
3
replies
932
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 16 months ago by ▴ 40 • written 16 months ago by • 0
0
votes
1
reply
990
views
minfi read.metharray.sheet error
minfi
updated 16 months ago by 65k • written 16 months ago by • 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 65k • written 20 months ago by • 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 ▴ 780 • written 23 months ago by • 0
0
votes
0
replies
917
views
Annotation Illumina Infinium Mouse Methylation
Illumina minfi IlluminaHumanMethylationEPICmanifest
2.0 years ago octaviompa • 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
0
replies
642
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 65k • written 2.2 years ago by • 0
0
votes
1
reply
881
views
EPIC ARRAY ANALYSIS
minfiDataEPIC #SexPrediction minfi
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by • 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 65k • written 2.7 years ago by • 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
869
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 ▴ 40 • written 3.1 years ago by • 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 • 0 • written 3.2 years ago by • 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
0
votes
9
replies
2.8k
views
Rhdf5lib installation problem
minfi Rhdf5lib
updated 3.3 years ago by ★ 6.5k • written 3.3 years ago by ▴ 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 50k • written 3.5 years ago by ▴ 20
0
votes
6
replies
1.5k
views
NaN values in beta/M values matrices of RGChannelSet are imputed during normalization?
minfiData methylationArrayAnalysis MethylationArrayData minfi
updated 3.5 years ago by ★ 6.5k • written 3.5 years ago by • 0
1
vote
3
replies
2.7k
views
normalization combination of noob + BMIQ/Quantile
minfi bmiq noob preprocessQuantile champ
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 50
0
votes
2
replies
1.0k
views
Convert MethyLumiSet into RGChannelSet (Illumina EPIC methylation data)
methylumi minfi microarray epic
4.1 years ago • updated 3.5 years ago Nala • 0
50 results • Page 1 of 1
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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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