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Where is 'constructOligoSetFrom' or 'constructOligoSetListFrom' function?
crlmm vanillaice
9.3 years ago Shi, Tao ▴ 720
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4
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Trouble following the first 5 lines of vanillaICE tutorial?
SNP6 crlmm vanillaice vanillaice crlmm cnv
updated 9.4 years ago by • 0 • written 9.4 years ago by ▴ 20
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Copy number analysis
SNP affy VanillaICE SNP affy VanillaICE
12.6 years ago Rob Scharpf ▴ 250
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2
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1.3k
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VanillaICE
Proteomics VanillaICE Proteomics VanillaICE
updated 12.9 years ago by ★ 6.8k • written 12.9 years ago by ▴ 110
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Annotation for Mouse Affy SNP arrays (MOUSEDIVm520650)?
Annotation Cancer VanillaICE crlmm Annotation Cancer VanillaICE crlmm
13.0 years ago Daniel Rico ▴ 110
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Question about using oligo and SNPchip for copy number analysis
SNP Cancer graph oligo SNPchip oligoClasses VanillaICE crlmm SNP Cancer graph oligo
15.4 years ago Min-Han Tan ▴ 40
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Creating a new instance of oligoSnpSet
Annotation Cancer Breast VanillaICE copynumber Annotation Cancer Breast VanillaICE
15.9 years ago Steven McKinney ▴ 310
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Answer: Annotation for EPICv2 by James W. MacDonald 67k
The CpG you point out is in the intronic region of SHANK2, so will not be in any of the locations you have in your barplot. ![enter ima…
Comment: WGCNA by Lluís Revilla Sancho ▴ 750
This is a question of a package outside Bioconductor, it would be best to ask to the maintainer. But i think he moved to industry and the w…
Comment: dmpFinder for other objects by James W. MacDonald 67k
Yes, but you should probably use M-values instead of betas (convert using `logit2`). However, `dmpFinder` is just a way to allow people to…
Comment: Highly DE genes but small count difference within conditions by Michael Love 42k
This last problem, I don't know how to help with, I think there's high variability here and not many degrees of freedom to overcome that
Answer: [DESeq2] Introduce a bias in DESeq2 by Michael Love 42k
This is often called an offset in statistical modeling. We have some support site posts about how to do this in DESeq2. Search for posts me…
Votes
Answer: Highly DE genes but small count difference within conditions
Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet
Trying to use enrichGO
Answer: edgeR 4.2.1 compression bug: a minimally reproducible snippet
Answer: dmpFinder for other objects
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