Bioconductor Matrix with covariables

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limma design matrix matrix with covariables

updated 6.8 years ago by Aaron Lun ★ 28k • written 6.8 years ago by michel655 • 0

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Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30

Thank you Gordon! Apologies if this is a too basic question-I'm a biologist and want to ensure I understand correctly. Here is my metadata …

Comment: nightmare to make custom txdb for genomes from ToxoDB by rohitsatyam102 ▴ 20

I offer my apologies if the title was misleading. I will change it at once. I wrote txdb because the error emnated from `seqlevelsStyle(txd…

Comment: nightmare to make custom txdb for genomes from ToxoDB by rohitsatyam102 ▴ 20

Hi Herve As I mentioned, for parasites we rely on VEuPathDB databases (such as ToxoDB here: https://toxodb.org/toxo/app/downloads) which p…

Comment: nightmare to make custom txdb for genomes from ToxoDB by Hervé Pagès 16k

`keepStandardChromosomes()` is not smart enough to know what to keep for this assembly. Note that what `keepStandardChromosomes()` means by…

Comment: nightmare to make custom txdb for genomes from ToxoDB by James W. MacDonald 67k

Thanks Hervé! Very helpful. However, I believe that `keepStandardChromosomes` gets called by `gDNAx`, and it appears not to work correctly.…

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