Showing : Methylation • reset
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Creating GRanges object
microarray minfi GenomicRatio GRanges Methylation
updated 6.6 years ago by 68k • written 6.6 years ago by • 0
1
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2
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1.8k
views
Methylation data visualization using methyAnalysis with minfi
methylation microarray illumina minfi methyanalysis
updated 6.7 years ago by ★ 1.3k • written 6.7 years ago by • 0
2
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1
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1.8k
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EPIC methylation array - analysis with ChAMP - how to export bed/wig file to view in UCSC/IGV?
methylation epic champ
updated 6.8 years ago by ▴ 290 • written 6.8 years ago by ▴ 10
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0
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1.1k
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All fragments/sequences captured using MeDIP are methylated?
medip-seq methylation CpGs
6.8 years ago saripalligautam86 ▴ 10
0
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2
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2.7k
views
ChAMP Normalization on EPIC Methylation Data
ChAMP Normalization FunctionalNormalization methylation EPIC
6.9 years ago yuabrahamliu • 0
1
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2
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2.4k
views
Minfi read.metharray.sheet error
minfi methylation dataimport minfidata missmethyl
updated 7.0 years ago by 68k • written 7.0 years ago by ▴ 20
2
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8
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2.7k
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edgeR: design matrix for methylation analysis
edger methylation
updated 7.0 years ago by 52k • written 7.2 years ago by • 0
0
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0
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1.1k
views
Error while using TCGAanalyze_DMR for >2 groups
methylation tcgabiolinks R gleason score TCGAanalyze_DMR
7.0 years ago mtkk94 • 0
5
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9
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2.3k
views
limma Multi-level Experiments correcting for continuous covariates
limma epic methylation limma design matrix covariates
updated 7.0 years ago by ★ 29k • written 7.0 years ago by • 0
0
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4
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1.6k
views
Taking relatedness among individuals into account in differential methylation analysis?
methylation minfi ChAMP
updated 7.0 years ago by ★ 6.5k • written 7.0 years ago by • 0
1
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2
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1.9k
views
Problem installing ChAMP package.
software error microarray champ methylation
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 10
0
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3
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2.0k
views
Minfi error when using force=TRUE in read.metharray
minfi methylation epic
7.1 years ago jbar3141 • 0
1
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1
reply
3.1k
views
Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
genomicfeatures genomation genomicranges methylation annotation
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by • 0
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0
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1.5k
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Interpretation of control strip and beta density plots for Illumina methylation array data using minFi
minfi methylation EPIC
7.1 years ago sichan • 0
0
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2
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1.6k
views
MethylKit DSS Package
R bioconductor methylation methylkit
updated 7.1 years ago by ▴ 20 • written 7.1 years ago by • 0
0
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0
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1.4k
views
Job: Post-doc in Prostate Cancer Research (Statistics / Computational Biology) at University of St Andrews (+PhD position also available)
cancer sequencing rnaseq methylation smallrna Job
7.2 years ago Andy Lynch ▴ 120
1
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1
reply
2.3k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names methylation illumina convertids
updated 7.3 years ago by 68k • written 7.3 years ago by ▴ 10
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0
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1.2k
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which value from ruvadj in missMethyl can present methylation status
methylation missmethyl RUV batch effect
7.3 years ago RC • 0
0
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0
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1.6k
views
DSS DMLTest Prior Estimate of theta dispersion
DSS dmltest bayesian statistics methylation
7.4 years ago floriandeckert ▴ 30
2
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3
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3.2k
views
"Seems your IDAT file not from one Array"
EPIC methylation ChAMP
updated 7.4 years ago by ▴ 30 • written 7.4 years ago by • 0
0
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6
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2.1k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
7.5 years ago dusan.petrovic • 0
2
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2
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1.9k
views
dmrseq: cannot adjust for a covariate
dmrseq dmr dmrs bisulfite methylation
updated 7.5 years ago by ▴ 60 • written 7.6 years ago by • 0
0
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0
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1.3k
views
differential methylation analysis with RnBeads
rnbeads methylation methylationepic dna methylation
7.5 years ago gabrielrfries • 0
0
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2
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2.4k
views
Error code using ChAMP/Bioconductor, unable to load data from EPIC methylation array
bioconductor methylation epic microarray champ
7.6 years ago csappleby-mallinder1 • 0
0
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2
replies
1.3k
views
methylPipe: how BSprepare handles zeros
methylation methylPipe
updated 7.8 years ago by ▴ 200 • written 7.8 years ago by • 0
0
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13
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3.2k
views
handling missing data (NA) for methylaion analysis in Limma
limma missing data methylation normalization
updated 7.9 years ago by ★ 29k • written 7.9 years ago by ▴ 10
0
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0
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993
views
About the meaning of the value column in minfi package
minfi methylation
8.1 years ago Antonio M. • 0
1
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3
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1.8k
views
Minfi returning incorrect beta values
minfi illumina illumina450k methylation R
8.2 years ago ezrabekele17 • 0
3
votes
1
reply
1.8k
views
Limma Model Design
limma methylation microarray
updated 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
1
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2
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2.1k
views
DMRcate results file ordered by genomic location and not Stouffer p-val?
DMRcate dmrcate methylation
updated 8.3 years ago by ▴ 230 • written 8.3 years ago by • 0
0
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0
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1.2k
views
minfi error with dmpfinder
methylation illumina
8.3 years ago indranipoddar • 0
0
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1
reply
2.2k
views
How to convert GenomicRatioSet to RGChannelSet in minfi::compartments()
minfi estimateCellCounts methylation
updated 8.3 years ago by ★ 6.5k • written 8.3 years ago by ▴ 10
0
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0
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945
views
Is there any way to parallelise sva functions?
sva methylation
8.3 years ago stewart999 ▴ 10
0
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6
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4.0k
views
difference in detection p-values from Minfi vs. GenomeStudio
minfi genomestudio methylation
updated 8.3 years ago by 68k • written 8.3 years ago by ▴ 40
0
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7
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3.9k
views
Is anyone able to explain the statistics behind the dmpFinder function in minfi package?
minfi methylation dmpfinder limma
updated 8.3 years ago by • 0 • written 9.0 years ago by ▴ 20
0
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2
replies
2.8k
views
Illumina methylationEPIC demo data in IDAT format?
methylation illumina EPIC methylationepic idat
updated 8.3 years ago by ★ 4.1k • written 8.3 years ago by • 0
0
votes
2
replies
1.9k
views
should i include PCs or MDSs as covariates in methylation study?
limma methylation R covariate MDS
updated 8.3 years ago by ★ 29k • written 8.3 years ago by • 0
1
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3
replies
1.9k
views
coef in dmrcate
dmrcate bumphunter methylation epic
updated 8.4 years ago by 68k • written 8.4 years ago by ▴ 10
1
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9
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4.6k
views
strange results from differential methylation analysis using limma
limma methylation methyanalysis IMA
updated 3.3 years ago by 21k • written 8.5 years ago by • 0
0
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1
reply
2.2k
views
Epigenetic clock (Horvath): package?
methylation illimina 450k methylation epigenetics minfi
updated 8.5 years ago by ▴ 60 • written 8.6 years ago by ▴ 120
0
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1
reply
1.6k
views
champ.load getting filtered RGChannelSet
champ methylation
updated 8.5 years ago by ▴ 90 • written 8.6 years ago by ▴ 20
0
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4
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2.1k
views
minfi "mapToGenome" dimension error
methylation epic microarray minfi methylationepic
8.5 years ago nhejazi • 0
0
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5
replies
2.8k
views
Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon methylation EPIC normalization
8.6 years ago Wade Davis ▴ 60
4
votes
4
replies
3.7k
views
bumphunter output clarification: p values achieved with b=1000: further correction needed?
methylation dmr analysis bumphunter
updated 8.7 years ago by 68k • written 8.7 years ago by • 0
0
votes
3
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1.7k
views
BiSeq. Model beta regression on resampled data.
biseq methylation dmr analysis
updated 8.7 years ago by ▴ 130 • written 8.7 years ago by • 0
0
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0
replies
1.4k
views
Bach effect and PEER/RUV correction on large population
methylation gene expression sva batch effect ruv
8.7 years ago carleshf ▴ 10
0
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0
replies
986
views
nPCs in minfi's Functional Normalization
minfi normalization methylation
8.7 years ago carlos.ruiz • 0
1
vote
4
replies
1.8k
views
M3D package in Bioconductor 3.4
bioconductor methylation
updated 8.7 years ago by ▴ 80 • written 8.8 years ago by • 0
0
votes
2
replies
2.6k
views
Error using Bumphunter and Block finder using CHAMP
champ methylation 450k
8.8 years ago • updated 8.7 years ago Bioinformatician_R ▴ 20
0
votes
0
replies
1.4k
views
Error in assay colnames when using readGEORawFile function in "minfi" package
minfi methylation 450k
8.8 years ago moonkinwen • 0
142 results • Page 2 of 3
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Comment: WGCNA analysis on RNAseq and proteoimcs data by sum31278 • 0
Hi sagigordon, Can you share how you performed WGCNA analysis for proteomics data? Thanks
Comment: European Bioconductor Conference 2023 planning by inadequate.peacock.iiag • 0
I once faced a dilemma similar to this when coordinating a smaller local event; despite initial hesitation, I learned invaluable skills and…
Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
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Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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