Showing : watermelon • reset
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A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
20 months ago calen.p.ryan • 0
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7
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1000
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Getting wrong rownames of MSet object when using pfilter from watermelon
wateRmelon Illumina EPIC pfilter
updated 4.4 years ago by • 0 • written 4.4 years ago by • 0
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3
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1.5k
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Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 4.7 years ago by ▴ 10 • written 4.7 years ago by • 0
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1.1k
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Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
5.2 years ago moldach ▴ 20
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1.5k
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MethylSet to MethyLumiSet
minfi methylumi watermelon
7.2 years ago Tom ▴ 10
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5
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2.2k
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Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon methylation EPIC normalization
7.3 years ago Wade Davis ▴ 60
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2
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1.4k
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Error while using BMIQ normalisation on a methylumiSet
limma watermelon methylumi bmiq
updated 7.4 years ago by ▴ 10 • written 7.4 years ago by ▴ 10
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2
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1.9k
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QC/normalization standards for cancer studies with 450k array data
minfi watermelon cancer 450k normalization
updated 8.8 years ago by ★ 6.5k • written 8.8 years ago by ▴ 10
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3
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minfi getProbeInfo error ( was WateRmelon betaqn error)
watermelon betaqn pfilter getProbeInfo minfi
9.2 years ago gctromp ▴ 10
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10
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2.2k
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MethyLumiM to MethyLumiSet?
convert lumi methylumi minfi wateRmelon convert lumi methylumi minfi wateRmelon
updated 10.5 years ago by ★ 4.2k • written 10.5 years ago by ▴ 190
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Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
Comment: Limma, eBayes different sample size of groups and adjustment by XW • 0
Could you explain more about how the analysis self-correct the different sample sizes when calling DEGs in limma? Thanks
Answer: How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy) by James W. MacDonald 65k
The section of the vignette that is *directly above the one you quote* says that you can use the HMMcopy utils to do all three things. And …
Comment: Help with error using camera() in limma by James W. MacDonald 65k
Again, this is where you need to read the help page and try to diagnose. It says ``` index: an index vector or a list of index vectors. …
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Comment: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Answer: Help with error using camera() in limma
Comment: Why p value inconsistent when using different number of pathway score?
Nominations for Bioconductor Awards 2024!
Awards • All
Scholar to James W. MacDonald 65k
Popular Question to jeffrey.maurer • 0
Centurion to Chris • 0
Commentator to Leonard Goldstein ▴ 200
Popular Question to Matthew Ritchie ▴ 1000
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