Bioconductor Ncrna

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computational biology molecular biology RNA r-loop ncRNA Job

6.2 years ago l.brown ▴ 10

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grch37 transcripts biotype biomaRt ncrna

updated 6.4 years ago by James W. MacDonald 67k • written 6.4 years ago by sergio.martinezcuesta ▴ 10

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gsea ncrna coexpression gene set analysis gene set testing

8.7 years ago m.fletcher ▴ 20

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biomart ncrna

updated 9.3 years ago by Thomas Maurel ▴ 800 • written 9.3 years ago by Zhang,Jiexin ▴ 20

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trna ncrna genomicfeatures featuredb biomart

updated 9.7 years ago by Hervé Pagès 16k • written 9.8 years ago by Keith Hughitt ▴ 180

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Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

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