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Question: differentially expressed miRNA using edge R
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gravatar for lily
10 weeks ago by
lily10
lily10 wrote:

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 ?? 

 

ADD COMMENTlink modified 10 weeks ago by Gordon Smyth32k • written 10 weeks ago by lily10
1
gravatar for Gordon Smyth
10 weeks ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

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 COMMENTlink modified 10 weeks ago • written 10 weeks ago by Gordon Smyth32k

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 REPLYlink written 10 weeks ago by lily10

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

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Gordon Smyth32k

Thanks. 

ADD REPLYlink written 10 weeks ago by lily10
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