Bioconductor ESet

Showing : eSet • reset

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12k

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microarray affy eset

updated 8.1 years ago by Gordon Smyth 52k • written 8.1 years ago by mathavanbioinfo ▴ 20

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9.0k

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eset annotation

updated 9.7 years ago by Diego Diez ▴ 760 • written 9.7 years ago by Vani ▴ 20

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1.9k

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biobase expressionset eset

updated 6.7 years ago by Martin Morgan 25k • written 6.7 years ago by andrew.birnberg ▴ 20

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1.7k

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subsetting eSet

9.0 years ago Shamim Sarhadi ▴ 20

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3.0k

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eset annotation

updated 9.7 years ago by James W. MacDonald 68k • written 9.7 years ago by colonppg ▴ 30

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10k

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limma differential expression design matrix error eset

updated 9.7 years ago by Aaron Lun ★ 28k • written 9.7 years ago by Vani ▴ 20

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1.5k

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affy eset

updated 4.2 years ago by James W. MacDonald 68k • written 4.2 years ago by AZ ▴ 30

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1.5k

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limma microarray eset

9.7 years ago Vani ▴ 20

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3.5k

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biobase eSet expressionSet

updated 8.4 years ago by Martin Morgan 25k • written 8.4 years ago by Guido Hooiveld ★ 4.1k

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4.5k

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methylumi eSet illuminahumanmethylation450k.db featureFilter

updated 9.8 years ago by James W. MacDonald 68k • written 9.8 years ago by martens.christopher • 0

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1.5k

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limma eset error ebayes

updated 9.7 years ago by James W. MacDonald 68k • written 9.7 years ago by Vani ▴ 20

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1.0k

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Minfi eset

7.2 years ago SplittingInfinity ▴ 60

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1.4k

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scan.upc eset

updated 9.6 years ago by Stephen Piccolo ▴ 600 • written 9.6 years ago by Jo ▴ 30

13 results • Page 1 of 1

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Replies

Comment: DiffBind custom normalization factor by Abbie • 0

Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…

Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k

All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…

Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0

Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…

Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k

For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…

Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k

I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …

Votes

A: Machine learning in R book

Data preparation and Machine learning on time course RNAseq data

Answer: Use of org.Rn.eg.db with GRCr8 reference genome

A: use tximport's countsFromAbundance when using DESeq2

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