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?

0

Entering edit mode

ZihaoXing • 0

@zihaoxing-13254

Last seen 2.6 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 • 409 views

ADD COMMENT • link updated 2.7 years ago by Gordon Smyth 43k • written 2.7 years ago by ZihaoXing • 0

score 1 · Answer 1 · 2018-09-23

1

Entering edit mode

Gordon Smyth 43k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

See edgeR's rpkm() function.

ADD COMMENT • link 2.7 years ago Gordon Smyth 43k

0

Entering edit mode

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 2.7 years ago ZihaoXing • 0