DESeq pvalue>0.05 qvalue=1

Question

[yueli7]

Hi,

I try to DESeq find the differentially expressed genes in two samples.

The result is all the pvalue>0.05, and qvalue=1.

Any suggestion or advice?

Thanks for great help!

Yue

[Michael Love]

it's discouraged to post simultaneously to multiple sites. it duplicates peoples effort in helping you, and splits up the answers.

https://support.bioconductor.org/p/70056/#70109

[poisonAlien]

Do you have replicates ?

[yueli7]

Hi poisonAlien,

Thank you for your post.

I do not have replicates.

Any suggestions or advice?

Thanks for help!

Yue

The format of my file is:

id    testis    soma
NV31416-RA    765    35458
TCONS_00021942    32896    678
NV12924-RA    2    20446
NV30843-RA    98    13609

[poisonAlien]

As Devon has replied below, without replicates its hard to do any differential expression. Maybe you could just use some sort of cutoff values for fold change to filter them.

[User 59]

Hi Yue,

If you wish to post large files as part of an question or comment please use http://pastebin.org or similar rather than pasting hundreds of lines into the text box. We didn't need all the lines to understand the format of your file!

[yueli7]

Thanks, everyone.

Thanks for everyone's great help!

Answer 1

[Devon Ryan]

Without biological replicates you have little hope of finding anything significant. Even if you did, the p-values in such comparisons need to be taken with a large grain of salt.

Answer 2

[alolex]

As Devon and poisonAlien have said, you can't calculate usable p-values without replicates. Thus, I would suggest doing a simple fold change calculation with a fold change cutoff for filtering. However, this should only be used for exploratory purposes and would not be publishable without biological replicates.

[andrew]

Totally agree!