SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Insert size important? 454andSolid De novo discovery 3 12-27-2017 01:33 AM
How to calculate P-value&FDR lynn012 RNA Sequencing 2 09-18-2011 10:51 PM
[Important] You can help SEQanswers to get published marcowanger General 0 08-14-2011 06:13 PM
Important fields of SAM file to be considered while compression nadir Bioinformatics 0 03-29-2011 09:58 PM
why is paired-end alignment support so important found Bioinformatics 1 03-03-2009 07:05 AM

Reply
 
Thread Tools
Old 01-27-2014, 10:25 AM   #21
raphael123
Member
 
Location: Mc Gill -- Montreal

Join Date: Dec 2013
Posts: 37
Lightbulb

p value is just a widely used joke. The signification of p value is hard to get and imply assumptions that lot of people don t know.
FDR is just a bigger joke. Your best pvalue will most of the time be multiply by your number of p value.
So if you have 10 genes to test giving you 10 pvalues, the best is multiply by 10, the second best by 5, then by 3.3333, then by 2.5, then by 2 etc .....

Here is the code in R

Code:
# produce a vector of FDR with an ordered pval vector
fdr = function(pval){
 size=length(pval)
 if(size<2) return(pval)

 #the worst pval is multiply by (size) / (size-1)
 FDR=c( min( 1 , pval[size]*(size)/(size-1)   ))

 for( i in 1:(size-1)) FDR=c(FDR,min(FDR[i] , pval[size-i]*(size)/(size-i)))

 # We have to revers the vector to be consistant
 return(rev(FDR))
}
raphael123 is offline   Reply With Quote
Old 01-27-2014, 11:39 AM   #22
rskr
Senior Member
 
Location: Santa Fe, NM

Join Date: Oct 2010
Posts: 250
Default

Quote:
Originally Posted by Simon Anders View Post
So, what do you suggest to do instead?
I don't know for sure. I first noticed the problem doing some meta-analysis hypothesis testing on coverage merging p-values of bases with each base having a different statistical power. Using Fishers meta-analysis procedure, it became obvious that the underpowered bases were dominating the the test and that Fishers test assumed all published results were adequately powered. It would be nice if that theory were also better. I came up with a heuristic involving weighted sums of -log(p-values) and information entropy as degrees of freedom, which has a certain appeal to it.
rskr is offline   Reply With Quote
Old 01-27-2014, 12:09 PM   #23
sindrle
Senior Member
 
Location: Norway

Join Date: Aug 2013
Posts: 266
Default

Quote:
Originally Posted by dpryan View Post
See the "genefilter" package for some useful functions.
Interesting, thanks!
Another question, excuse my ignorance.. But look at these codes:

> FDR <- p.adjust(lrt$table$PValue, method="BH")
> sum(FDR < 0.05)

Is this the way to choose FDR < 0.1:

> FDR <- p.adjust(lrt$table$PValue, method="BH")
> sum(FDR < 0.1)
sindrle is offline   Reply With Quote
Old 02-07-2014, 08:58 AM   #24
csmatyi
Member
 
Location: Nebraska

Join Date: Oct 2011
Posts: 25
Default

Quote:
Originally Posted by swbarnes2 View Post
I feel that this is an appropriate contribution:

http://xkcd.com/882/
oh it's so appropriate
csmatyi 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 09:17 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO