Problems encountered while using methylKit

[梁文秀]

I found that the q value in the file of methylKit output DMC is the same value：0.0232810229810332, is this situation normal? How should I solve this problem?

Here's the code I used：

file.list = list("N0_CpG.txt","N24_CpG.txt","M0_CpG.txt","M24_CpG.txt")

myobj=methRead(file.list,

               sample.id=list("N0","N24","M0","M24"), 

               assembly="mm10",

               treatment=c(0,1,1,1), 

               context="CpG", 

filtered.myobj=filterByCoverage(myobj,lo.count=10,lo.perc=NULL,

                               hi.count=NULL,hi.perc=99.9) 

normalized.myobj <- normalizeCoverage(filtered.myobj)

meth=unite(normalized.myobj, destrand=FALSE)

meth1=reorganize(meth,sample.ids = c("N24","N0"),treatment=c(1,0))

myDiff1=calculateDiffMeth(meth1) 

write.table(myDiff1,"N24_N0_DMC.txt",quote = F,sep = '\t',row.names = FALSE)

myDiff1.hyper=getMethylDiff(myDiff1,difference=25,qvalue=0.05,type="hyper")

myDiff1.hypo=getMethylDiff(myDiff1,difference=25,qvalue=0.05,type="hypo")

myDiff1.all=getMethylDiff(myDiff1,difference=25,qvalue=0.05)

write.table(myDiff1.all,"N24_N0_DMC_all.txt",quote = F,sep = '\t',row.names = FALSE)

write.table(myDiff1.hyper,"N24_N0_DMC_hyperl.txt",quote = F,sep = '\t',row.names = FALSE)

write.table(myDiff1.hypo,"N24_N0_DMC_hypo.txt",quote = F,sep = '\t',row.names = FALSE)

Looking forward to your reply, thank you！

[alex....@gmail.com]

Hi,

A possible reason for the same q-value could be too few significant differences: 

If there are very few differentially methylated cytosines detected, the multiple testing correction (to calculate the q-value) could result in the same q-value for all DMCs. This might happen because, with a limited number of tests, the p-values are adjusted similarly.

By default methylkit adjusts the p-value using the SLIM method,  if you want you could try different methods to correct the p-values for multiple testing. For other methods see p.adjust function. 

Best,  

Alex