Question

how to output and get the normalization gene expression data (similar to the FPKM gene expression data) from reads count data by DESeq2 and edgeR?

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ZihaoXing • 0

@zihaoxing-13254

Last seen 3.5 years ago

the RNAseq read counts data can do the different RNAseq expression by the DESeq2 and edgeR , but i also want to get the normalization gene expression data such as FPKM data ,and do the later clinical survival analysis with gene expression. can i get the normalization gene expression by edgeR and DESeq2 data.

deseq2 edger fpkm counts TCGA • 554 views

ADD COMMENT • link updated 3.7 years ago by Gordon Smyth 45k • written 3.7 years ago by ZihaoXing • 0

score 1 · Answer 1 · 2018-09-23

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Gordon Smyth 45k

@gordon-smyth

Last seen 34 minutes ago

WEHI, Melbourne, Australia

See edgeR's rpkm() function.

ADD COMMENT • link 3.7 years ago Gordon Smyth 45k

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thanks Gordon Smyth ,i try to use the rpkm() function to see the transform results. thanks your advice. hope you work happy and well on your research.

ADD REPLY • link 3.7 years ago ZihaoXing • 0