Hello BioConductor world,


I am doing a time course study using Affymetrix microarrays. I have three time points (0, 4, and 6 hours) and a control and treatment. There is no treatment at 0 hours because the genes would be the same. I am able to get the significant transcripts, but I can not create the heat maps I want. I have searched the literature and the internet and have not found what I was looking for.  I would like two heat maps: one for the controls versus treatments for the different time points (two columns or groups, 4 and 6 hr) and the second heat map comparing the different times (three columns or groups, 0 to 4 and 6 hr and 4 to 6 hr). What would be the best way to do this? Is there a way to combine the the results from the different microarrays in the same control or treatment to form one column instead of the multiple columns? Looking at other heat maps, I could not find an example of the combined columns.   I have about 200 different transcripts for the the controls versus treatments for the different time. Is there a way to select the number of genes in the heat map.  I may be think about the heat maps wrong, so if I am what is the best way to think about heat maps and the code or instructions, for a new person, for the right type of heat map.


Here is my code (control time [c0, c4, c6] or treatment time[t4,t6]):


library(affy)

library(limma)


targets = readTargets("time course.txt")

raw = ReadAffy(filenames=targets$FileName)

data = read.AnnotatedDataFrame("time course.txt", sep="", fill=TRUE)

phenoData(raw) = data[sampleNames(raw),]

RMA = rma(raw)


lev = c("c0","c4","t4","c6","t6")

f = factor(data$Target, levels=lev)

design = model.matrix(~0+f)

colnames(design) = lev

fit = lmFit(RMA, design)

cont.wt = makeContrasts(

    "t4-c4",

    "t6-c6",

    c0t4 = c0-(t4-c4),

    c0t6 = c0-(t6-c6),

    t4t6 = (t4-c4)-(t6-c6),

    levels=design)

fit2 = contrasts.fit(fit, cont.wt)

fit2 = eBayes(fit2)


results = classifyTestsF(fit2, p.value=0.05)

summary(results)


Thank you in advance.

Andrew Block
Graduate Student
Nebraska Center of Virology
University of Nebraska at Lincoln

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