User: grant.dejong

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Posts by grant.dejong

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Comment: C: edgeR or DESeq2 between duplicated chromosomes in the same individual
... Hi Gordon, I'm sorry for any confusion! I'm looking at an allopolyploid (which has undergone a recent whole-genome duplication event via inter-specific hybridization) and am particularly interested in comparing gene expression between each gene pair. These genes are organized in large, highly simila ...
written 6 weeks ago by grant.dejong0
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Comment: C: edgeR or DESeq2 between duplicated chromosomes in the same individual
... Sorry, by RPK/FPK I'm referring normalization of my raw counts by gene length in kilobases (raw counts/(gene length/1000)). Since edegR and DESeq2 internally correct for library size I figured representing my data by FPK/RPK would be acceptable but a colleague brought up the fact that I shouldn't us ...
written 6 weeks ago by grant.dejong0
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edgeR or DESeq2 between duplicated chromosomes in the same individual
... Hi there, I have an RNA-seq dataset from a polyploid species (consisting of sets of similar chromosomes, which consequently, contain highly similar paralogs). I'd like to know whether I could compare expression between these gene pairs using the aforementioned software. Is there a way to incorpor ...
normalization edger deseq2 dge written 6 weeks ago by grant.dejong0 • updated 6 weeks ago by Gordon Smyth39k

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