Question: fold-change and FDR p-value threshold for miRNA (small RNA-Seq) data
0
gravatar for Edalat
3.1 years ago by
Edalat30
Edalat30 wrote:

HI, I am analyzing miRNA (small RNA analysis) data and I would like to establish a fold-change and p-value threshold which is biologically significant.with Fold change ≥ 1.5 and FDR P-VALUE ≤ .05, I lose most of miRNA.

rna-seq • 1.5k views
ADD COMMENTlink modified 3.1 years ago by kanwarjag1000 • written 3.1 years ago by Edalat30
1
gravatar for kanwarjag
3.1 years ago by
kanwarjag1000
United States
kanwarjag1000 wrote:

Fold change may not be best as some microrNAs will have zero values in one case while very large value in another case. you can still calculate the FC by transforming values, but I think p value may be best, you can use DEseq, EdgeR or even simple t test.

ADD COMMENTlink written 3.1 years ago by kanwarjag1000

thank you for attention. with FDR P-VALUE ≤ .05 of t-test (without fold change) , I lose most of miRNA too, I think to use bigger p value?

ADD REPLYlink written 3.1 years ago by Edalat30

Then I will see how many replicates you have. It looks like you have few replicates and which do not show a good correlation with in a group

ADD REPLYlink written 3.1 years ago by kanwarjag1000

excuse me which is better for filtering miRNA ,FDR P-value or P-value?

ADD REPLYlink written 3.1 years ago by Edalat30
1

I read many things about being cautious with p-value then I prefer FRD

ADD REPLYlink written 3.1 years ago by A3.5k
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