[BioC] limma Time Course Experiments question

[Marcelo Laia]

Hi,

I have did an analysis like limma 8.8 section "Time Course Experiments"

I will paste the text here and after I will make a question.

> lev <- c("wt.0hr","wt.6hr","wt.24hr","mu.0hr","mu.6hr","mu.24hr")
> f <- factor(targets$Target, levels=lev)
> design <- model.matrix(~0+f)
> colnames(design) <- lev
> fit <- lmFit(eset, design)

   Which genes respond at either the 6 hour or 24 hour times in the
wild-type? We can find
these by extracting the contrasts between the wild-type times.

> cont.wt <- makeContrasts(
+      "wt.6hr-wt.0hr",
+      "wt.24hr-wt.6hr",
+ levels=design)
> fit2 <- contrasts.fit(fit, cont.wt)
> fit2 <- eBayes(fit2)
> topTableF(fit2, adjust="BH")

Any two contrasts between the three times would give the same result.
The same gene list
would be obtained had "wt.24hr-wt.0hr" been used in place of
"wt.24hr-wt.6hr" for example.

   Which genes respond in the mutant?

> cont.mu <- makeContrasts(
+      "mu.6hr-mu.0hr",
+      "mu.24hr-wt.6hr",
+ levels=design)
> fit2 <- contrasts.fit(fit, cont.mu)
> fit2 <- eBayes(fit2)
> topTableF(fit2, adjust="BH")

   Which genes respond differently in the mutant relative to the wild-type?

> cont.dif <- makeContrasts(
+     Dif6hr =(mu.6hr-mu.0hr)-(wt.6hr-wt.0hr),
+     Dif24hr=(mu.24hr-mu.6hr)-(wt.24hr-wt.6hr),
+ levels=design)
> fit2 <- contrasts.fit(fit, cont.dif)
> fit2 <- eBayes(fit2)
> topTableF(fit2, adjust="BH")

topTableF give me something like this:

         ID      wt.0hr  wt.6hr  F        P.Value   adj.P.Val
248   B-1:7  -0.27    -3.23  27.30  4.16e-08  0.000
360   B-2:9  -0.08    -2.62  23.10  2.56e-07  0.000
1999 I-16:8  -0.82     3.00  19.11  1.72e-06  0.001
487   C-1:6  -0.02    -2.92  18.99  1.82e-06  0.001
201   A-6:1   1.21    -3.36  18.92  1.89e-06  0.001

What the values in the columns wt.0hr and wt.6hr means? I could
consider these values like fold change? For example, gene B-1:7 is
3.23 log fold change down regulate in time 6hr in relation to time
0hr. And in relation to time 24hr?

If the contrasts "wt.24hr-wt.0hr" and "wt.24hr-wt.6hr" are equals, how
I could know if gene B-1:7 is more expressed in time 6 than time 24,
for example?

Is there a way to plot a graph with expression in y-axis and time on
x-axis for differentially expressed genes? How I could do this for
this example?

Thank you very much

-- 
Marcelo Luiz de Laia
Universidade do Estado de Santa Catarina
UDESC - www.cav.udesc.br
Lages - SC - Brazil
Linux user number 487797
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