Bioconductor WateRmelon

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731

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DNAMethylation wateRmelon Computation minfi

2.4 years ago calen.p.ryan • 0

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1.3k

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wateRmelon Illumina EPIC pfilter

updated 5.1 years ago by lschal • 0 • written 5.1 years ago by anne-kristin.stavrum • 0

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1.8k

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wateRmelon minfi methylation pfilter preprocessNoob

updated 5.3 years ago by tgorri ▴ 10 • written 5.3 years ago by sara.blocquiaux • 0

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1.3k

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methylation ENmix BMIQ wateRmelon

5.9 years ago • updated 5.8 years ago moldach ▴ 20

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1.7k

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minfi methylumi watermelon

7.9 years ago Tom ▴ 10

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2.5k

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wateRmelon methylation EPIC normalization

7.9 years ago Wade Davis ▴ 60

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1.7k

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limma watermelon methylumi bmiq

updated 8.0 years ago by tgorri ▴ 10 • written 8.0 years ago by poojitha.stemcell ▴ 10

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2.1k

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minfi watermelon cancer 450k normalization

updated 9.4 years ago by Kasper Daniel Hansen ★ 6.5k • written 9.4 years ago by metamaden ▴ 10

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2.3k

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watermelon betaqn pfilter getProbeInfo minfi

9.9 years ago gctromp ▴ 10

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2.5k

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convert lumi methylumi minfi wateRmelon convert lumi methylumi minfi wateRmelon

updated 11.1 years ago by Tim Triche ★ 4.2k • written 11.1 years ago by Martin Rijlaarsdam ▴ 190

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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0

Thanks for your reply!

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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