Question: DESeq pvalue>0.05 qvalue=1
0
gravatar for yueli7
4.1 years ago by
yueli740
China
yueli740 wrote:

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

deseq pvalue qvalue • 1.4k views
ADD COMMENTlink modified 4.1 years ago by Michael Love1.9k • written 4.1 years ago by yueli740
1

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

ADD REPLYlink written 4.1 years ago by Michael Love1.9k

Do you have replicates ?

ADD REPLYlink written 4.1 years ago by poisonAlien2.8k

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
ADD REPLYlink modified 6 weeks ago by RamRS23k • written 4.1 years ago by yueli740
1

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.

ADD REPLYlink written 4.1 years ago by poisonAlien2.8k

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!

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Daniel Swan13k

Thanks,everyone.

 

Thanks for everyone's great help!

ADD REPLYlink written 4.1 years ago by yueli740
6
gravatar for Devon Ryan
4.1 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

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.

ADD COMMENTlink written 4.1 years ago by Devon Ryan91k
1
gravatar for alolex
4.1 years ago by
alolex890
United States
alolex890 wrote:

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.

ADD COMMENTlink written 4.1 years ago by alolex890

Totally agree!

ADD REPLYlink written 4.1 years ago by andrew460
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