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1.1k

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Normalization probe affy affydata limma marray BEAT Normalization probe affy affydata

updated 18.3 years ago by Wolfgang Huber 13k • written 18.3 years ago by Gordon Smyth 48k

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1.0k

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SNP GO Network BEAT SNP GO Network BEAT

20.4 years ago DevNet ▴ 20

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814

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Normalization GO probe affy affydata vsn limma marray BEAT Normalization GO probe affy

18.3 years ago Naomi Altman ★ 6.0k

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803

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affy oligo BEAT affy oligo BEAT

18.2 years ago Naomi Altman ★ 6.0k

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1.1k

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Category BEAT Category BEAT

10.3 years ago Hin-Tak Leung ▴ 30

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Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

Votes

Comment: Batch correction and repeated measures

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

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