Question: verboseScatterplot generate cor and pvalue not same as moduleTraitCor
0
gravatar for joseph.houjue
2.3 years ago by
joseph.houjue0 wrote:

Dear all,

I have the code as this:

Define numbers of genes and samples

 nGenes = ncol(VAX_Expr)
 nSamples = nrow(VAX_Expr)

Recalculate MEs (1st principal component) with color labels

 MEs0 = moduleEigengenes(VAX_Expr, moduleColors)$eigengenes

ME is the correlation matrix of module and sample, by row is sample, by column is module

 MEs = orderMEs(MEs0)

make correlation btween module and trait

 moduleTraitCor = cor(MEs, VAX_Bench, use = "p")
 moduleTraitPvalue = corPvalueStudent(moduleTraitCor, nSamples)

The correlation value btw trait and module can be found in the moduleTraitCor, however, when I plot GS vs MM, the cor and corp is not the same in the moduleTraitCor and moduleTraitPvalue.

Caculate the module membership (GS for each module)

  geneModuleMembership = as.data.frame(cor(VAX_Expr, MEs, use = "p"))
  MMPvalue = as.data.frame(corPvalueStudent(as.matrix(geneModuleMembership), nSamples))

names (colors) of the modules

  modNames = substring(names(MEs), 3)

  names(geneModuleMembership) = paste("MM", modNames, sep="")
  names(MMPvalue) = paste("p.MM", modNames, sep="")

  module = "brown"
  column = match(module, modNames)    
  moduleGenes = moduleColors == module     
  verboseScatterplot(abs(geneModuleMembership[moduleGenes,column]),
                     abs(df_geneTraitGS[moduleGenes,1]),
                     xlab = paste("Module Membership in", module, "module"),
                     ylab = c("Gene significance"),
                     main = paste("Module membership vs. Gene significance\n"),
                     cex.main = 1.2, cex.lab = 1.2, cex.axis = 1.2, 
                     pch = 21, col = "black", bg = module)
wgcna • 954 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.3 years ago by joseph.houjue0

I don't understand the question, what is not the same, could you post the numeric differences between them (and where do you calculate each?)

ADD REPLYlink written 2.2 years ago by LluĂ­s R.840

There is a new related question, here: Module membership vs gene significance does not correlate (WGCNA)

ADD REPLYlink written 5 months ago by Kevin Blighe46k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1685 users visited in the last hour