Question: Differential expression in time series
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gravatar for peter robinson
12.5 years ago by
peter robinson300 wrote:
Hi, I was wondering if anyone could give me pointers for the following situation. Given a time course data series with 3-4 repeats for individual time points, what is the best way of determining a list of differentially expressed genes for each time point (possibly compared to the zero time point)? I can think of several ways of going about this, but I have not been able to find very much in the literature I have consulted (perhaps I am looking in the wrong place). Thanks in advance, Peter
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ADD COMMENTlink modified 12.5 years ago by James W. MacDonald51k • written 12.5 years ago by peter robinson300
Answer: Differential expression in time series
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gravatar for James W. MacDonald
12.5 years ago by
United States
James W. MacDonald51k wrote:
Hi Peter, Peter Robinson wrote: > Hi, > > I was wondering if anyone could give me pointers for the following > situation. Given a time course data series with 3-4 repeats for > individual time points, what is the best way of determining a list of > differentially expressed genes for each time point (possibly compared > to the zero time point)? I can think of several ways of going about > this, but I have not been able to find very much in the literature I > have consulted (perhaps I am looking in the wrong place). Have you looked at the limma user's guide? There is at least one example of a time course analysis there. You might also use the BioC taskViews pages. For instance, there is one for TimeCourse experiments here: http://www.bioconductor.org/packages/2.0/TimeCourse.html Best, Jim > > Thanks in advance, Peter > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 12.5 years ago by James W. MacDonald51k
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ADD REPLYlink written 12.5 years ago by Lev Soinov470
Hi Lev, Lev Soinov wrote: > Dear List, > On the page 49 of the LIMMA user guide there is an example of how to make a difference of differences in experiments with several factors: > > "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")" > > I use a very similar code to find differences between time effects and strain effects. > I have two strains (B and W) and two different time points (2 and 1 hours). I am trying to find genes which respond differently: > 1. in B vs W, when comparing time points 1 and 2 (i.e. I compare BvsW in time point 1 to BvsW in time point 2) > 2. in time in different strains (i.e. I compare B1vsB2 versus W1vsW2) > > I am getting the same results, or they should be the same? > Could you comment on whether this is a right way to analyse time series? It appears you want to test for the interaction between time and strain. Both of your points (1 and 2 above) are essentially identical. You want to know what genes react differently over time in the two strains (and worded differently, but meaning the same thing - what genes react differently between the strains at different times). These two things are verbo-algebraically the same (yup, new word. My next move is to start a new Wikipedia entry describing exactly what it means ;-D) > > My code is below. > > > Thank you, > Lev. > > > temp<-rma(data) > > targets <- readTargets("Targets.txt") > >>lev <- c("W.1","B.1","W.2","B.2") >>f <- factor(targets$Target, levels=lev) >>design <- model.matrix(~0+f) >>colnames(design) <- lev >>fit <- lmFit(temp, design) >>cont.dif <- makeContrasts(Diff.Time=(B.2-W.2)-(B.1-W.1), Diff.Strain=(B.2-B.1)-(W.2-W.1), levels=design) As the statements above are verbo-algebraically the same, these two terms are algebraically the same. (B.2-W.2)-(B.1-W.1) = (B.2-B.1)-(W.2-W.1) Hence you should get the same results from each contrast. And yes, this contrast does give you the interaction. Best, Jim >>fit2 <- contrasts.fit(fit, cont.dif) >>fit2 <- eBayes(fit2) > > > I am getting the same results for both coefficients: > >>results<-decideTests(fit2, method="separate", p=0.01, lfc=1) >>summary(results) > > Diff.Time Diff.Strain > -1 61 61 > 0 44951 44951 > 1 89 89 > > My target file is: > FileName Target > 3517 W.1 > 3518 W.1 > 3519 W.1 > 3520 W.1 > 3521 W.1 > 3522 B.1 > 3524 B.1 > 3525 B.1 > 3526 B.1 > 3527 W.2 > 3528 W.2 > 3529 W.2 > 3530 W.2 > 3531 B.2 > 3532 B.2 > 3533 B.2 > 3534 B.2 > > > > --------------------------------- > Yahoo! Mail is the world's favourite email. Don't settle for less, sign up for your freeaccount today. -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD REPLYlink written 12.5 years ago by James W. MacDonald51k
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