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GDCdow tcgabiolinks error tcgadownload download_error

updated 4.8 years ago by Tiago Chedraoui Silva ▴ 260 • written 4.8 years ago by miki716 • 0

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tcgadownload deseq2 mirna normalization

updated 5.3 years ago by Lorena Pantano ▴ 120 • written 5.3 years ago by Björn • 0

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R tcgabiolinks tcgadownload error

6.3 years ago juniuskcc • 0

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tcgabiolinks tcga tcgadownload gdcprepare gdc

updated 6.5 years ago by Tiago Chedraoui Silva ▴ 260 • written 6.7 years ago by enigmargs • 0

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tcgabiolinks tcgadownload

updated 6.9 years ago by Tiago Chedraoui Silva ▴ 260 • written 6.9 years ago by Leonardo Collado Torres ★ 1.0k

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tcgabiolinks tcgadownload

updated 2.3 years ago by H. Z. Amini ▴ 10 • written 7.2 years ago by sabarinath.chandrasekharan ▴ 10

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tcgabiolinks TCGAdownload

updated 7.2 years ago by Tiago C. Silva ▴ 270 • written 7.3 years ago by roladali ▴ 20

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tcgadownload

7.2 years ago maedakus ▴ 10

8 results • Page 1 of 1

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Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq by Michael Love 40k

Did you manually calculate RPMs? Try `fpm(dds)` for comparison, as this also uses DESeq2 median ratio scaling.

Comment: collapseReplicates error after tximeta by Michael Love 40k

A note: I've now changed collapseReplicates() to output a loud warning when it is run on a DESeqDataSet (SummarizedExperiment) with more th…

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 …

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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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