Showing : MethylationArray • reset
6
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6
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1.5k
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Limma Paired Analysis - Force intercept to 0
MethylationArray limma
3.3 years ago • updated 3.2 years ago MoltenLight ▴ 10
5
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5
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780
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
2
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2
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1.2k
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
2.0 years ago fluentin44 • 0
2
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6
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1.1k
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 12 months ago by ▴ 170 • written 12 months ago by • 0
2
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1
reply
648
views
Limma model orientation
limma methylation MethylationArray
updated 24 months ago by 65k • written 24 months ago by • 0
2
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7
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2.4k
views
Blood cell composition adjustment in methylation EPIC array: ChAMP
MethylationArray methylationArrayAnalysis ChAMP
updated 6 months ago by • 0 • written 3.4 years ago by ▴ 20
1
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6
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454
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Library size normalization in methylation count analysis
edgeR MethylationArray
8 weeks ago mico • 0
1
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4
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442
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EPIC or EPICv2 demo data of brain samples. FlowSorted.DLPFC.EPIC Availability?
DNAMethylation MethylationArray methylationArrayAnalysis illumina
11 weeks ago mikat • 0
1
vote
2
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304
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
11 weeks ago mico • 0
1
vote
0
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156
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Rnaseq sample barcode does not match barcode from TCGA Methylation data
TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data
8 weeks ago BioinfoMug • 0
1
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1
reply
552
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 11 months ago by ▴ 40 • written 12 months ago by • 0
1
vote
1
reply
270
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 9 weeks ago by 65k • written 9 weeks ago by • 0
0
votes
0
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138
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TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData
7 weeks ago • updated 5 weeks ago Giovanni Calice ▴ 160
0
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0
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959
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Surrogate variable, celltype composition correction and overfitting in DNA methylation data
sva limma methylation MethylationArray
3.3 years ago epibio ▴ 10
0
votes
1
reply
237
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Error in GOmeth function of missMethyl when EPICv2 annotation is used
DNAMethylation GO MethylationArray missMethyl EPICv2
updated 7 weeks ago by ▴ 40 • written 7 weeks ago by • 0
0
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1
reply
717
views
EPIC v2 demo data from blood samples
MethylationArray methylationArrayAnalysis
updated 6 months ago by 65k • written 6 months ago by • 0
0
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5
replies
1.2k
views
minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 13 months ago by • 0
0
votes
1
reply
536
views
LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 12 months ago by 50k • written 13 months ago by • 0
0
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4
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1.0k
views
Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 13 months ago by 65k • written 13 months ago by • 0
0
votes
7
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428
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
0
votes
11
replies
702
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
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0
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611
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
3.4 years ago coobzie • 0
22 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Are you commenting on the OP's question, or adding a different question? If the latter, please start a new post rather than piggybacking on…
Answer: Math expression in shapeCustom legend in EnhancedVolcano by James W. MacDonald 65k
Use `bquote`. See section 4.6 in [the vignette][1]. [1]: https://bioconductor.org/packages/release/bioc/vignettes/EnhancedVolcano/in…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
I was thinking about removing unwanted variations at the sample level (ie a transformation shared across genes) not at the gene level. Corr…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
That's an assumption used for normalization of a sample, not an assumption you can use for an individual model. We always normalize to atte…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by SamGG ▴ 350
Is useless the assumption that the majority of genes have no variation in expression (bearing in mind that they are distributed over the en…
Votes
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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