SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
p-value and log fold change Bidfudge Bioinformatics 3 07-25-2016 04:00 AM
RPKM vs Fold Change ppm Bioinformatics 4 05-06-2014 08:49 AM
Log fold change Erwan Bioinformatics 3 03-25-2014 06:05 AM
Standardized Fold Change dbaud Introductions 5 01-27-2014 11:47 AM
fold change value-cuffdiff madsaan Bioinformatics 4 02-10-2011 07:51 AM

Reply
 
Thread Tools
Old 04-02-2017, 06:32 PM   #1
renuka22
Member
 
Location: US

Join Date: Mar 2017
Posts: 22
Default p-value and fold change

Hello,

I got my rna-seq analysis from the company and they have assigned p-value to each gene. Is it possible to have a p-value from only one set of data since I had sent only one batch and there were no replicates? Also, some of my genes have p>0.05 (not differentially expressed) but high fold-change increase. So which of the two should be considered important - p-value or fold change?

Thanks
renuka22 is offline   Reply With Quote
Old 04-03-2017, 02:10 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

If you only sent them single samples from your groups then the p-values are largely meaningless. There's not a direct correspondence between fold-change and p-value, since lowly expressed genes will randomly show higher fold-changes (i.e., the p-value is a function of expression level and fold change).
dpryan is offline   Reply With Quote
Old 04-03-2017, 08:35 AM   #3
renuka22
Member
 
Location: US

Join Date: Mar 2017
Posts: 22
Default

Ok. But can the p-value be between my control and treatment samples as this is what they mentioned in their analysis and p<0.05 means those genes are differentially expressed?

Thanks
renuka22 is offline   Reply With Quote
Old 04-04-2017, 12:50 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

The presumption is that the p-value is from a poisson test, so yes it's between the two samples.

Yes, p<0.05 would normally mean differentially expressed, aside from the fact that the p-values in your case are largely meaningless.
dpryan is offline   Reply With Quote
Old 04-04-2017, 12:22 PM   #5
renuka22
Member
 
Location: US

Join Date: Mar 2017
Posts: 22
Default

So I guess the p-value is between technical replicates hence meaningless. Thanks a lot!
renuka22 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:32 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO