Question: FPKM significant value
0
gravatar for samh
3.8 years ago by
samh0
malaysia
samh0 wrote:

Hi
I have done expression analysis using cufflinks, Can anybody here tell me what exactly FPKM significant values for RNAseq.
tq.  

rna-seq • 2.0k views
ADD COMMENTlink modified 3.8 years ago by Devon Ryan90k • written 3.8 years ago by samh0

By significant you mean genes that are expressed or differential expression between samples?

ADD REPLYlink written 3.8 years ago by roy.granit800

I means the genes that are expressed. 

ADD REPLYlink written 3.8 years ago by samh0

You might want to add that as a comment instead of an answer as now this post is listed as "Answered".

On the other note, do you have any ERCC control within your samples? If not, people usually just arbitrarily select a threshold for "expressed"

 

ADD REPLYlink written 3.8 years ago by Sam2.3k

Thank you for the reminder :) , I dont have any ERCC control within my samples and I will select a threshold for "expressed".

ADD REPLYlink written 3.8 years ago by samh0

You might want to read this post:

How Do You Justify Your Rna-Seq Expression Threshold (Fpkm/Rpkm) ?

 

ADD REPLYlink written 3.8 years ago by Sam2.3k
1
gravatar for Devon Ryan
3.8 years ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

About the only method that I've seen that doesn't require spike-ins is the one described in this paper, which is actually fairly similar to what I think a number of us had been informally recommending to people (nice to see that someone made a real paper out of it).

ADD COMMENTlink written 3.8 years ago by Devon Ryan90k
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