Showing : symbol • reset
5
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7
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2.0k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 2.7 years ago by 48k • written 2.7 years ago by • 0
2
votes
1
reply
809
views
biomaRt fails to retrieve GO description for some particular gene
biomart go r bioconductor symbol
4.1 years ago foehn ▴ 80
6
votes
5
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4.4k
views
biomaRt Ensembl gene ID to multiple HGNC symbol
ensembl symbol hgnc biomart
updated 4.4 years ago by 63k • written 4.4 years ago by ▴ 80
0
votes
1
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1.0k
views
error in getsymbol function
symbol
updated 6.5 years ago by ★ 3.7k • written 6.5 years ago by • 0
0
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0
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1.0k
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Using Pathview with gene.idtype = "SYMBOL"
Pathview symbol
7.1 years ago sofia.figueiredo ▴ 10
3
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3
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1.5k
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Does AnnotationHub replaces AnnotationDbi for ID conversion (e.g. entrez, refseq, symbols)?
conversion symbol entrez
updated 8.0 years ago by 63k • written 8.0 years ago by ▴ 50
6 results • Page 1 of 1
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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…
Votes
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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