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Question: design contrast in limma package for microarray expression data
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gravatar for sup230
12 weeks ago by
sup23010
sup23010 wrote:

Hi, 

I just wanted to get confirmation that the following code would get me the result I wanted. So I am interested in getting the list of differential expressed genes between two groups between seizure YES and seizure NO. The expression set is the microarray data and seizure information is in the affy.clinic.sz data frame "seizure" column.

design.sz<-model.matrix(0~affy.clinic.sz$seizure)
colnamesdesign.sz)<-c("NO", "YES")

fit.sz<-lmFitaffy.eset.sz, design.sz)

contrasts<-makeContrasts(YES-NO, levels = design.sz)
fit.sz2<-contrasts.fitfit.sz, contrasts)

topTable(fit.sz2, adjust.method = "BH", sort.by = "logFC")

 

Will this list give me the list of DE genes comparing seizure YES group to NO group, where negative logFC value indicates that the gene's expression is higher in seizure NO group and positive logFC indicates that the gene's expression is higher in sz YES group?

Thank you for your help in advance!!

ADD COMMENTlink modified 12 weeks ago by Aaron Lun17k • written 12 weeks ago by sup23010
1
gravatar for Aaron Lun
12 weeks ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

Your interpretation of the sign of the log-fold change is correct, but there are a number of issues with your code:

  • Setting 0~affy.clinic.sz doesn't make sense, I assume you mean ~0 + affy.clinic.sz.
  • You're missing opening brackets throughout.
  • You need to run eBayes after contrasts.fit.
  • Set p.value=0.05 in topTable to get DE genes at a FDR of 5%, or set number=Inf and subset later.
ADD COMMENTlink modified 12 weeks ago • written 12 weeks ago by Aaron Lun17k
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