Showing : MethylationArray • reset
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Methylation data - different probes are classified differently based on transcript? (Illumina methylation arrays, using minfi)
minf minfiDataEPIC MethylationArrayData MethylationArray EPICv2manifest
4 weeks ago charlie.wright • 0
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178
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Unable to find sample sheet file for ChAMP methylation data analysis
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 6 weeks ago by 68k • written 6 weeks ago by • 0
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2
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383
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
3 months ago Meghan • 0
2
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1
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458
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Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 5 months ago by 68k • written 5 months ago by ▴ 10
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706
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In the sesame package, what does the estimate output mean from testEnrichment()
MethylationArray methylation sesame methylationArrayAnalysis
5 months ago ramiro.barrantes ▴ 10
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421
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Annotating DMRs
MethylationArray MethylationArrayData methylationArrayAnalysis
updated 6 months ago by 68k • written 6 months ago by ▴ 10
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1
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517
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Empty Results from champ.DMP Despite Expected Output
MethylationArray ChAMP R
updated 6 months ago by 68k • written 6 months ago by • 0
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3
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597
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Open Sesame: in what genes are my differentially methylated probes!!
MethylationArray sesameData sesame
updated 3 months ago by • 0 • written 6 months ago by ▴ 10
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2
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701
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save.rnb.set warnings when trying to save rnb.set
RnBeads RnBeads.hg19 MethylationArray
written 7 months ago by • 0
0
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1
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649
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ChAMP analysis Error: Meth Matrix and UnMeth Matrix seems not paried correctly AND incomplete final line
MethylationArray methylationArrayAnalysis ChAMP
updated 3 months ago by • 0 • written 8 months ago by • 0
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2
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1.4k
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Batch effect correction: methylome data
sesame BatchEffect MethylationArray
updated 10 months ago by ▴ 20 • written 10 months ago by • 0
3
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2
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871
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limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 9 months ago by 52k • written 10 months ago by • 0
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2
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1.7k
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Get genomic coordinates of CpGs sites (chromosomes, genomic position)
GenomeWideAssociation SequenceAnnotation MethylationArray GenomicDistributionsData
10 months ago Yveto • 0
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0
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461
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
12 months ago • updated 11 months ago Giovanni Calice ▴ 160
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3
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1.8k
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
12 months ago • updated 5 months ago s.malik • 0
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11
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1.4k
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 12 months ago by 52k • written 12 months ago by • 0
1
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7
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1.3k
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Library size normalization in methylation count analysis
edgeR MethylationArray
updated 4 months ago by • 0 • written 12 months ago by • 0
1
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1
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1.3k
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Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 12 months ago by 68k • written 12 months ago by • 0
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7
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1.1k
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error in reading idat files and creating rgset
minfi MethylationArray
updated 13 months ago by 68k • written 13 months ago by • 0
1
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2
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850
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
13 months ago mico • 0
1
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4
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1.2k
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
13 months ago mikat • 0
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1
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1.2k
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EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 17 months ago by 68k • written 17 months ago by • 0
5
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5
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1.3k
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
19 months ago Jitendra ▴ 10
1
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1
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859
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 22 months ago by ▴ 40 • written 22 months ago by • 0
2
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6
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1.6k
views
cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 22 months ago by ▴ 230 • written 22 months ago by • 0
0
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1
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846
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 23 months ago by 52k • written 23 months ago by • 0
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4
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1.6k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
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5
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1.9k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 2.0 years ago by • 0
2
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1
reply
910
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Limma model orientation
limma methylation MethylationArray
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
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2
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1.7k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
2.9 years ago fluentin44 • 0
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0
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1.2k
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
4.1 years ago epibio ▴ 10
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6
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2.0k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
4.2 years ago • updated 4.1 years ago MoltenLight ▴ 10
2
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7
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3.3k
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Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 17 months ago by • 0 • written 4.2 years ago by ▴ 20
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792
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
4.3 years ago coobzie • 0
34 results • Page 1 of 1
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Answer: Using tximport for kallisto aligned TOIL data by James W. MacDonald 68k
If you just have the transcript data, you probably don't need (and maybe cannot use) `tximport`. Instead you could just do the naive thing …
Answer: Reading gene expression data in GPR format and converting it to xlsx format by James W. MacDonald 68k
Setting aside the inadvisability of putting these data into Excel (and I should point out that these data are not single-cell, but instead …
Comment: concentration tables suitable as input for new packages? by wilkinson • 0
I am grateful for your response. Software such as "Spectra" may parse MS-data to generate tables of concentrations, for instance. But inste…
Comment: Removing UTR from GTF for gene quantification by ATpoint ★ 4.7k
Consider asking at biostars or bioinformatics reddit, since this is not directly related to a Bioconductor problem. Anyway, a couple of th…
Comment: Combining RNAseq and microarray data using edgeR/limma-voom by Hoover • 0
I got it! ([Drift Boss][1]) [1]: https://driftbossgame.co
Votes
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
How to remove genes with 0 counts in tximport?
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