Showing : wateRmelon • reset
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A survey of computational setups for Illumina Infinium DNA methylation EPIC array pipeline
DNAMethylation wateRmelon Computation minfi
2.7 years ago calen.p.ryan • 0
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7
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1.5k
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Getting wrong rownames of MSet object when using pfilter from watermelon
wateRmelon Illumina EPIC pfilter
updated 5.5 years ago by • 0 • written 5.5 years ago by • 0
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3
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2.0k
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Combining pfilter (wateRmelon) and preprocessNoob (minfi)
wateRmelon minfi methylation pfilter preprocessNoob
updated 5.7 years ago by ▴ 10 • written 5.7 years ago by • 0
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1.4k
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Error in ENmix::bmiq.mc(): BMIQ estimates encountered error, try to run it again
methylation ENmix BMIQ wateRmelon
6.2 years ago moldach ▴ 20
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1
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1.8k
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MethylSet to MethyLumiSet
minfi methylumi watermelon
8.2 years ago Tom ▴ 10
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5
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2.7k
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Different errors when attempting to normalize using wateRmelon (v1.1.18)
wateRmelon methylation EPIC normalization
8.3 years ago Wade Davis ▴ 60
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2
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1.8k
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Error while using BMIQ normalisation on a methylumiSet
limma watermelon methylumi bmiq
updated 8.4 years ago by ▴ 10 • written 8.4 years ago by ▴ 10
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2
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2.2k
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QC/normalization standards for cancer studies with 450k array data
minfi watermelon cancer 450k normalization
updated 9.8 years ago by ★ 6.5k • written 9.8 years ago by ▴ 10
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3
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2.5k
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minfi getProbeInfo error ( was WateRmelon betaqn error)
watermelon betaqn pfilter getProbeInfo minfi
10.2 years ago gctromp ▴ 10
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10
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2.7k
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MethyLumiM to MethyLumiSet?
convert lumi methylumi minfi wateRmelon convert lumi methylumi minfi wateRmelon
updated 11.5 years ago by ★ 4.2k • written 11.5 years ago by ▴ 190
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Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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