Off topic:making contrast in limma for Affymetrix data
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Jamal • 0
@jamal-13612
Last seen 5.1 years ago


hi guys,  I want to create a contrasts matrix to compare the Affymetrix array (two types of genotypes, two treatment groups (infected) and controls for each genotype and three times for each genotype), for comparison, I wrote the code below Please guide. Where is the problem?

TF <- paste(P1$Genotype, P1$Time, P1$Treatment, sep=".")
TF <- factor(TF)
design <- model.matrix(~0+TF)              
fit <- lmFit(exprs(ndata.raw), design)

cont.matrix <- makeContrasts(
        q1= q.1.E - q.1.C,
        q6= q.6.E - q.6.C,
        q24= q.24.E - q.24.C,
        Q1= Q.1.E - Q.1.C,
        Q6= Q.6.E - Q.6.C,
        Q24= Q.24.E - Q.24.C,
        Diff_1h = (Q.1.E - Q.1.C) - (q.1.E - q.1.C),
        Diff_6h = (Q.6.E - Q.6.C) - (q.6.E - q.6.C),
        Diff_24h = (Q.24.E - Q.24.C) - (q.24.E - q.24.C),
        levels=design)

Is this part of the code (Diff_24h = (Q.24.E - Q.24.C) - (q.24.E - q.24.C))  is correct to compare the two genotypes?

affymetrix microarray Limma design and contrast matrix contrast matrix • 607 views
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