DESeq pvalue>0.05 qvalue=1
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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.
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Ram
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Devon Ryan
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Devon Ryan
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.
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Do you have replicates ?
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:
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.
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!
Thanks, everyone.
Thanks for everyone's great help!
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