
Similar Threads  
Thread  Thread Starter  Forum  Replies  Last Post 
volcano plots cummeRbund  godzilla07  Bioinformatics  8  02042015 01:55 PM 
Are Cuffdiff qvalues and pvalues reliable when multiple treatments are analyzed?  gwilymh  Bioinformatics  1  03162014 12:32 PM 
cummeRbund diffData() or fpkm() values  jeales  Bioinformatics  0  06262013 07:29 AM 
CummeRbund csDendro error: "need finite ylim values" when replicates=TRUE  mebbert  Bioinformatics  4  07182012 09:22 AM 
beginning of quality values record not found & qual length () differs from seq length  papori  Bioinformatics  1  07092012 01:25 PM 

Thread Tools 
04272014, 10:13 PM  #1 
Member
Location: Kansas City Join Date: Jan 2014
Posts: 18

Inquiry: pvalues & qvalues for cummeRbund volcano?
Hi,
Suppose I have the following command: Code:
sigGene < csVolcano(genes(cuffData), "A, "B") Code:
sigGene < csVolcano(genes(cuffData), "A, "B", alpha = 0.01, showSignificant =T) GeekyOmega PS  I looked at the bioconductor manual for cummeRbund. What is the default alpha for csVolcano()? Is it alpha = 0.05 for pvalue/qvalue? I can't figure out how it works exactly in the default/manual situation. Thanks. 
07082014, 06:18 AM  #2 
Member
Location: Istanbul, Turkey Join Date: Oct 2012
Posts: 28

Hello Hyates,
Depending on the output, I can say alpha is for qvalue. But in the volcano plot it is the corresponding pvalue. If your cutoff for qvalue is 0.01 you should see that red dots for pvalue starts around log(2.42) in volcano plot (it would be exactly at 2.00 if alpha was accounted for pvalue). 
Tags 
cuffdiff, cummerbund, r language, volcano plot 
Thread Tools  

