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Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
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updated 5.0 years ago by
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written 5.0 years ago by
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updated 4.8 years ago by
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updated 21 months ago by
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2.0 years ago • updated 23 months ago
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updated 5.2 years ago by
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written 5.2 years ago by
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Comment: Finding DEGs by using edgeR
by
Gordon Smyth
50k
Filtering (removing lowly expressed genes) is separate to normalization.
It isn't clear why not subsetting would cause any difficulty. It …
Comment: How to make DGEList and design matrix by edgeR package
by
prity6459
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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
•
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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
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Gordon Smyth
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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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