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Accessing local installation of biomart results in "Unexpected format to the list of available marts"
mart martconfigurator biomaRt xml
updated 2.8 years ago by ★ 6.1k • written 2.8 years ago by • 0
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News: Ensembl 100 has been released
biomart ensembl e100 mart news News
3.4 years ago Thomas Maurel ▴ 790
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Error in martCheck(mart, c("ensembl", "ENSEMBL_MART_ENSEMBL")) : No dataset selected, please select a dataset first.
biomart mart ensembl
updated 3.5 years ago by 63k • written 3.5 years ago by • 0
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News: Ensembl 99 has been released and renaming of species
biomart ensembl e99 mart news News
3.7 years ago Thomas Maurel ▴ 790
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0
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699
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News: Ensembl 98 has been released and renaming of species
biomart ensembl e98 mart News
4.0 years ago Thomas Maurel ▴ 790
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4
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901
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retrieve vgnc gene name or vgnc gene symbol from Biomart after differential analysis
biomart mart getbm
updated 5.2 years ago by 63k • written 5.2 years ago by ▴ 20
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News: Ensembl release 85 is out!
ensembl biomart release85 ensembl release mart News
7.2 years ago Thomas Maurel ▴ 790
4
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9
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News: Ensembl release 84 is out!
ensembl mart release84 biomart ensembl release News
updated 7.4 years ago by ▴ 20 • written 7.6 years ago by ▴ 790
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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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