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Choosing appropriate FPKM cutoff for finding differential expressed genes

Hi every body,

I want to analyze the results of Cuffdiff.

Cuffdiff has detected 149 significant differential expressed genes.

However, some genes have FPKM=0 (no read has been mapped) or very small FPKM in one condition.

My question is, should I consider those with FPKM=0 or very small FPKM?

Is it biologically possible that one genes does not expressed in one condition and over expressed in another condition?

I am looking forward your comments

Regards

Nazanin

fpkm cutoff cuffdiff
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updated by Biostar Biostar • written by nazaninhoseinkhan nazaninhoseinkhan

Dear Nazanin, Hi.

There are some scripts for Filtering "Transcripts Based on Expression Values".

About "Is it biologically possible . . . " in the RNA-seq experiments, I guess the answer could be yes according to case/control condition, but FPKM=0 may has another reason

~ Best

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written by Farbod Farbod

Hello nazaninhoseinkhan!

We believe that this post does not fit the main topic of this site.

Closed after 3 years.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

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