Showing : MethylationArray • reset
2
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7
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2.4k
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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
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
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
0
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5
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1.2k
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minfi error read.metharray.exp
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
written 13 months ago by • 0
2
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6
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1.0k
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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
0
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4
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999
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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
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0
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957
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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
5
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5
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779
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limma output for epic array methylation data
linearregression epicarray MethylationArray limma
8 months ago Jitendra ▴ 10
0
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1
reply
712
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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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11
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699
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Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
2
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1
reply
646
views
Limma model orientation
limma methylation MethylationArray
updated 24 months ago by 65k • written 24 months ago by • 0
0
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0
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610
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Diffrential Gene expression in a group of specific methylated prometor patience
GeneExpression methyAnalysis MethylationArray
3.4 years ago coobzie • 0
1
vote
1
reply
549
views
urgent error for producing table of topGO() annotated DMPs methylation
methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray
updated 11 months ago by ▴ 40 • written 11 months ago by • 0
0
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1
reply
533
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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
1
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6
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451
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Library size normalization in methylation count analysis
edgeR MethylationArray
8 weeks ago mico • 0
1
vote
4
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437
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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
0
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7
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425
views
error in reading idat files and creating rgset
minfi MethylationArray
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
1
vote
2
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303
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How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
11 weeks ago • updated 10 weeks ago mico • 0
1
vote
1
reply
267
views
Need Advice: Issue with ChAMP Analysis - Meth and UnMeth Matrix Pairing Error
MethylationArray methylationArrayAnalysis ChAMP
updated 8 weeks ago by 65k • written 8 weeks ago by • 0
0
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1
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235
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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
1
vote
0
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154
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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
0
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0
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136
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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
22 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
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