Bioconductor MethylationArray

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139

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MethylationArray normalize450K TCGAbiolinks Normalization MethylationArrayData

7 weeks ago • updated 5 weeks ago Giovanni Calice ▴ 160

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702

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edgeR MethylationArray

updated 7 weeks ago by Gordon Smyth 50k • written 8 weeks ago by mico • 0

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238

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DNAMethylation GO MethylationArray missMethyl EPICv2

updated 7 weeks ago by belinda.phipson ▴ 40 • written 7 weeks ago by s.malik • 0

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456

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edgeR MethylationArray

8 weeks ago mico • 0

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158

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TCGAMethylation450k MethylationArray TCGAbiolinks Tcga TCGAbiolinksGUI.data

8 weeks ago BioinfoMug • 0

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272

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MethylationArray methylationArrayAnalysis ChAMP

updated 9 weeks ago by James W. MacDonald 65k • written 9 weeks ago by david.cheishvili • 0

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429

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minfi MethylationArray

updated 10 weeks ago by James W. MacDonald 65k • written 10 weeks ago by sharangiiv • 0

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307

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edgeR MethylationArray

11 weeks ago mico • 0

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443

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DNAMethylation MethylationArray methylationArrayAnalysis illumina

11 weeks ago mikat • 0

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2.4k

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MethylationArray methylationArrayAnalysis ChAMP

updated 6 months ago by dorota.komar • 0 • written 3.4 years ago by Ankit ▴ 20

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719

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MethylationArray methylationArrayAnalysis

updated 6 months ago by James W. MacDonald 65k • written 6 months ago by henry-keen • 0

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781

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linearregression epicarray MethylationArray limma

8 months ago Jitendra ▴ 10

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552

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methylationArrayAnalysis topGO missMethyl MethylationArrayData MethylationArray

updated 12 months ago by belinda.phipson ▴ 40 • written 12 months ago by Grace • 0

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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10

Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…

Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k

Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…

Answer: ATACseq merge peaks by ATpoint ★ 4.0k

That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10

Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k

I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…

Votes

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length

Comment: Deseq2. decontXcounts not integers. Useful alternative?

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)

biomaRt error: database disk image is malformed

Comment: biomaRt : No lock file for BiocFileCache

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Popular Question to James W. MacDonald 65k

Scholar to Michael Love 41k

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