Showing : MethylationArrayData • reset
3
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6
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326
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Methylation data analysis
MethylationArrayData methylationArrayAnalysis
26 days ago • updated 24 days ago aldea85 • 0
1
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3
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320
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Merging Methylation data (M-values) with phenotypic data
MethylationArrayData methylationArrayAnalysis
updated 3 months ago by 64k • written 3 months ago by • 0
0
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1
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259
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Read methylation data from tar files on GEO (GSE73303)
GeneExpression Bioconductor GEOquery MethylationArrayData
4 months ago Arianna • 0
1
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2
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454
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How to perform a methylation analyisis from m values
MethylationArrayData methylationArrayAnalysis
6 months ago Irene • 0
1
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1
reply
408
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urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 7 months ago by ▴ 40 • written 7 months ago by • 0
2
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6
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794
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cpg.annotate() in DMRcate error
DNAMethylation methylationArrayAnalysis DMRcate MethylationArrayData MethylationArray
updated 7 months ago by ▴ 160 • written 7 months ago by • 0
0
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1
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342
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LmFit error in EPIC methylation array analysis, Minfi
methylationArrayAnalysis minfi MethylationArrayData minfiDataEPIC MethylationArray
updated 8 months ago by 49k • written 8 months ago by • 0
0
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4
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673
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 9 months ago by 64k • written 9 months ago by • 0
0
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5
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716
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 9 months ago by • 0
0
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2
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952
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ChAMP package:Error in cmdscale(d) : 'k' must be in {1, 2, .. n - 1}
MethylationArrayData
13 months ago shuangshuang • 0
2
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2
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969
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Limma vs. lm for methylation data
limma MethylationArrayData MethylationArray
20 months ago fluentin44 • 0
0
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0
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596
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filtering options in RnBeads for array data
Epigenetics RnBeads MethylationArrayData methylationArrayAnalysis
20 months ago Jitendra ▴ 10
0
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0
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688
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Problem loading Red channel idat files with champ.load
R MethylationArrayData ChAMP
2.0 years ago Paulina • 0
0
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0
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592
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DNA methylation EPIC array and ChromHMM
chromhmmData MethylationArrayData
2.3 years ago macsue.jacques ▴ 10
0
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0
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598
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minfi - estimateCellCounts2-proportions sum more than 1
minfi minfiData MethylationArrayData
2.3 years ago ponche_de_kiwi • 0
0
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6
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2.9k
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Merge problems in R
methylationArrayAnalysis ChAMP MethylationArrayData
2.4 years ago FWNL15 • 0
0
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1
reply
766
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Error in reading metharray sheet
DifferentialMethylation MethylationArrayData
updated 2.5 years ago by ▴ 740 • written 2.5 years ago by • 0
0
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0
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868
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How to get illumina CpG IDs by gene name?
MethylationArrayData RnBeads
2.8 years ago D • 0
1
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4
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2.2k
views
Unable to read in the IDAT files using read.metharray.exp()
MethylationArrayData methy Bioconductor minfi
2.8 years ago shweta • 0
1
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1
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1.1k
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DMR Plot
dmr MethylationArrayData DMRcatedata
updated 3.1 years ago by 64k • written 3.1 years ago by • 0
20 results • Page 1 of 1
Recent ...
Replies
Comment: Can the limma package be applied to Log2 RUV-normalized data? by Shaimaa Gamal • 0
I see. Do you recommend a certain method to get norm.factors through calcNormFactors function espcially if the downstream analysis includes…
Comment: Can the limma package be applied to Log2 RUV-normalized data? by Gordon Smyth 49k
515 samples is certainly large enough.
Comment: Correct the batch effect in methylation analysis in R by kyj2226 • 0
Thank you for your kind response Gordon! :) Have a good time at the end of the year! Best, Yujin Kim
Comment: Agilent Microarray Gene Oncology analysis gone wrong by SamGG ▴ 320
Gordon said to let coef to its default value: topTable(fit, n=20)
Comment: Can the limma package be applied to Log2 RUV-normalized data? by Shaimaa Gamal • 0
Hi Gordon, On what basis we can determine whether the dataset is large or not? I am working on a dataset of 515 samples and 5440 genes. I w…
Votes
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Comment: Can the limma package be applied to Log2 RUV-normalized data?
Answer: Correct the batch effect in methylation analysis in R
Comment: Why is DMRcate not available for Bioconductor version 3.18?
Answer: Correct the batch effect in methylation analysis in R
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