Showing : wateRmelon • reset
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A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
2.2 years ago calen.p.ryan • 0
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7
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1.2k
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Getting wrong rownames of MSet object when using pfilter from watermelon
wateRmelon Illumina EPIC pfilter
updated 4.9 years ago by • 0 • written 4.9 years ago by • 0
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1.7k
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Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 5.1 years ago by ▴ 10 • written 5.1 years ago by • 0
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1.3k
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Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
5.7 years ago • updated 5.6 years ago moldach ▴ 20
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1.6k
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MethylSet to MethyLumiSet
minfi methylumi watermelon
7.7 years ago Tom ▴ 10
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5
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2.5k
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Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon methylation EPIC normalization
7.8 years ago Wade Davis ▴ 60
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1.6k
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Error while using BMIQ normalisation on a methylumiSet
limma watermelon methylumi bmiq
updated 7.8 years ago by ▴ 10 • written 7.8 years ago by ▴ 10
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2
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2.0k
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QC/normalization standards for cancer studies with 450k array data
minfi watermelon cancer 450k normalization
updated 9.3 years ago by ★ 6.5k • written 9.3 years ago by ▴ 10
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3
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2.3k
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minfi getProbeInfo error ( was WateRmelon betaqn error)
watermelon betaqn pfilter getProbeInfo minfi
9.7 years ago gctromp ▴ 10
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10
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2.5k
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MethyLumiM to MethyLumiSet?
convert lumi methylumi minfi wateRmelon convert lumi methylumi minfi wateRmelon
updated 10.9 years ago by ★ 4.2k • written 11.0 years ago by ▴ 190
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Answer: Automatically generate contrasts from a model matrix / formula by Gordon Smyth 51k
I am very concerned that you are attempting to extract pairwise comparisons from an interaction formula like `0 + Group*Sex + Age`, because…
Comment: Mostly increased counts in differentially accessible peaks using DESeq2 by Ricardo Iván • 0
Hi Michael, Thanks for your reply. After reviewing the PCAs, maybe the issue that despite the replicates looking similar, there is still a…
Comment: Using Normalized Counts in DESeq2 by Michael Love 42k
Also, just to add, there are many dozens of posts on this topic of DESeq2 applied to TCGA counts, normalized or other. Recommend google sea…
Answer: Using Normalized Counts in DESeq2 by ATpoint ★ 4.5k
TCGA raw counts can be obtained for example using the TCGAbiolinks or recount packages.
Comment: How to reverse complement some elements of a DNAStringSet by Christine Jones • 0
Fantastic, thank you
Votes
Answer: When running contrasts, does it use normalized read counts?
Comment: featureCounts fails to load annotation file
Answer: How to reverse complement some elements of a DNAStringSet
Answer: KEGGgraph result difference
Answer: What should be the normalization protocol for RNA seq data for WGCNA?
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