Question

differentially expressed miRNA using edge R

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lily ▴ 20

@lily-11438

Last seen 3.5 years ago

India

hi

i have downloaded miRNA-seq RPKM-log data from TCGA portal. If i want to find the differentially expressed miRNA , can i used directly RPKM data or do i need to change to CPM ??

edger • 1.4k views

ADD COMMENT • link updated 7.2 years ago by Gordon Smyth 51k • written 7.2 years ago by lily ▴ 20

score 1 · Answer 1 · 2017-09-06

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Gordon Smyth 51k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

edgeR requires counts, so neither RPKM or CPM will do the job.

From page 14 of the edgeR Users' guide:

users should not transform the read counts in any way before inputing them to edgeR. For example, users should not enter RPKM or FPKM values to edgeR in place of read counts. Such quantities will prevent edgeR from correctly estimating the mean-variance relationship in the data, which is a crucial to the statistical strategies underlying edgeR. Similarly, users should not add artificial values to the counts before inputing them to edgeR.

See also Differential expression of RNA-seq data using limma and voom()

ADD COMMENT • link 7.2 years ago Gordon Smyth 51k

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Thanks for the reply. One more doubt, read counts and raw counts are the same. If i have the raw counts then can i used edge R to get DEmiRNA ??

ADD REPLY • link 7.2 years ago lily ▴ 20

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Yes, read counts and raw counts are the same, and you can use edgeR to analyse them.