Bioconductor Spectral counts

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spectral counts proteomics limma edger deseq

updated 8.2 years ago by Gordon Smyth 48k • written 8.2 years ago by eleonoregravier ▴ 70

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limma voom proteomics spectral counts massspectrometry

updated 8.7 years ago by Gordon Smyth 48k • written 8.7 years ago by Ben Neely ▴ 40

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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…

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

I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…

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batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Answer: Batch correction and repeated measures

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