Bioconductor Edger

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DGEList edgeR

1 hour ago • updated 33 minutes ago prity6459 • 0

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subsettingdata edgeR designmatrix

updated 5 minutes ago by Gordon Smyth 50k • written 16 hours ago by prity6459 • 0

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limma edgeR RNASeq

updated 1 hour ago by Gordon Smyth 50k • written 1 day ago by Shaimaa Gamal • 0

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128

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edgeR

updated just now by Gordon Smyth 50k • written 1 day ago by Jonathan ▴ 10

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7.7k

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deseq2 edgeR rna-seq

updated 19 hours ago by Elizabeth • 0 • written 8.8 years ago by gthm ▴ 30

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Comment: Finding DEGs by using edgeR by Gordon Smyth 50k

Filtering (removing lowly expressed genes) has nothing to do with normalization. It isn't clear why not subsetting would cause any difficu…

Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0

Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…

Comment: Finding DEGs by using edgeR by prity6459 • 0

Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …

Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k

It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…

Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k

Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…

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Answer: OrgDb for maize

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