[BioC] Limma time course analysis - defining comparisons

[Helen Zhou]

Dear Marta,

thank you for your suggestion. I am sorry it has taken
me so long to reply.
I have had a look at the masigpro package, but it
seems to be specificaly for shorter time courses,
whereas my real data set has 6 time points. Am I wrong
about this? The example shown below is just because it
was with public data available in bioconductor.
I have also seen someone mention the package
"timecourse". Does anyone on this list have any
recomendations about that?

Thank you
Helen

--- MARTA AGUDO BARRIUSO <martabar at um.es> wrote:

> 
> you may try masigpro package, it has been designed
> exactly to extract  
> those "changing a little bit each time point"-genes
> 
> Helen Zhou <zhou.helen at yahoo.com> escribi�
> 
> > Dear Jim
> >
> > Thanks you for your answer. As I understand you
> are
> > recommending me to do direct comparisons between
> for
> > example 12-4h and 24-12h. However, could there not
> in
> > theory be a gene that was up a little bit in
> 12vs4h
> > and 24vs12h, so that the difference for neither of
> > these would be large enough to be significant, but
> for
> > 24vs4h the combined change might be significant?
> In
> > that case I guess I would need all 3 comparisons?
> >
> > Thanks you
> > Helen
> >
> > --- "James W. MacDonald" <jmacdon at med.umich.edu>
> > wrote:
> >
> >> Hi Helen,
> >>
> >> Helen Zhou wrote:
> >> > Dear Sir/Madam
> >> >
> >> > I am trying to analyse a short time series,
> >> roughly
> >> > following section 8.8 in the limma user guide.
> I
> >> am
> >> > interested in differences between all time
> points.
> >> I
> >> > am not sure whether I have to make all the
> >> pariwise
> >> > comparisons directly, or whether they can be
> done
> >> > indirectly as well.
> >> >
> >> > For example, if I want to compare to time
> points,
> >> what
> >> > is the differences between the two methods
> listed
> >> > below.
> >> >
> >> > library(bronchialIL13)
> >> > # Just for the IL13 samples
> >> > data <- HAHrma[,7:15]
> >> > # Design
> >> > targets	<-
> >> >
> >>
> >
>
c("h12","h12","h12","h24","h24","h24","h4","h4","h4")
> >> > lev	<- c("h12","h24","h4")
> >> > f	<- factor(targets, levels=lev)
> >> > design	<- model.matrix(~0+f)
> >> > colnames(design)	<- lev
> >> > fit <- lmFit(data, design)
> >> > # 2-step contrasts, used to indirectly get 24
> to 4
> >> > hours as well as the other two comparisons
> >> > contrasts <- makeContrasts("h24-h12", "h12-h4",
> >> > levels=design)
> >> > fit2 <- contrasts.fit(fit, contrasts)
> >> > fit2 <- eBayes(fit2)
> >> > # Direct contrast of 24 to 4 hours
> >> > contrasts2 <- makeContrasts("h24-h4",
> >> levels=design)
> >> > fit3 <- contrasts.fit(fit, contrasts2)
> >> > fit3 <- eBayes(fit3)
> >> > # Comparison
> >> > topTable(fit2, coef=1:2)
> >> > topTable(fit3, coef=1)
> >>
> >> In the first case you are asking the question
> 'which
> >> reporters are
> >> different in either h24 vs h4 _or_ h12 vs h4',
> >> whereas in the second
> >> case you are asking 'which reporters are
> different
> >> between H24 and h4'.
> >>
> >> It is entirely possible that you could have a
> gene
> >> that isn't different
> >> between h24 and h4, but is different at h12. This
> >> would show up in the
> >> first comparison but not the second, so if you
> want
> >> to compare time
> >> points you are better off making direct contrasts
> >> rather than using the
> >> F-statistic for multiple contrasts (which will
> then
> >> require the
> >> additional step of figuring out which contrast(s)
> >> caused the statistic
> >> to be significant).
> >>
> >> Best,
> >>
> >> Jim
> >>
> >>
> >> >
> >> > More or less the same probe sets are present,
> but
> >> in
> >> > different order and with different p values. Is
> >> the
> >> > difference because using coef=1:2 will go via
> an
> >> > F-test? And if I want the change from 24h-0h as
> >> well
> >> > as 42-12h and 12-4h, is it most correct for me
> to
> >> > specify that contrast directly? In my actual
> >> > experiment I have 4 time points, so will it be
> >> enough
> >> > for me with 3 possible comparisons, or will I
> have
> >> to
> >> > write all the 6 possible combinations?
> >> >
> >> > Thank you in advance for all your help.
> >> >
> >> > Yours truly
> >> > Mrs Helen Zhou
> >> >
> >> > P.S. I think this might have been mentioned on
> the
> >> > list before, but I could not find the email. In
> >> that
> >> > case, please excuse me for repeating this.
> >> >
> >> > _______________________________________________
> >> > 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
> >>
> >
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> >
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> >
> 
> 
> 
>