DGE for non model

Question

[loly.pearl86]

Hello,

I would like to ask about DGE Why some research use FDR , P value, and log2 fold-change value (≤0,05) and other chose the value less than <0.01when they want to find the DEG

My question is depend on what it should be chosen?

I hope if some one can explain it for me as i am doing DGE for the first time

Answer 1

[Farbod]

Dear loly.pearl86 , Hi.

please have look at:

https://groups.google.com/forum/#!msg/trinityrnaseq-users/T9VBfIAMbjU/N-4nCrBKEgAJ;context-place=forum/trinityrnaseq-users

[loly.pearl86]

Thanks i will have a look

cheers

Answer 2

[Devon Ryan]

Some people even use (adjusted) p<0.1, the threshold to use depends on how much of a false-positive rate you can afford in subsequent experiments.

[loly.pearl86]

Thanks , but most of what i read was useing FDR <0.05