Bioconductor Rsqlite

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RSQLite org.Hs.eg.db

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RSQLite lumi

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jaspar rsqlite

updated 5.6 years ago by James W. MacDonald 63k • written 5.6 years ago by m.d.shapiro • 0

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R RSQLite

updated 6.2 years ago by James W. MacDonald 63k • written 6.2 years ago by biostR ▴ 10

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reactome.db rsqlite

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rsqlite

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rsqlite bioconductor bioclite rcpp.h

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oligo rsqlite pd.hta.2.0

updated 7.0 years ago by James W. MacDonald 63k • written 7.0 years ago by Vincent J. Carey, Jr. 6.7k

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org.hs.eg.db DBI rsqlite

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annotation annotationdbi rsqlite

8.5 years ago Ceca Bojic ▴ 10

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biocinstaller genomicfeatures rsqlite

updated 8.8 years ago by Dan Tenenbaum ★ 8.2k • written 8.8 years ago by vimartin • 0

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VariantAnnotation RSQLite

8.8 years ago remi.tournebize ▴ 10

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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

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

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

Answer: Batch correction and repeated measures

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