[BioC] affycoretools: group parameter

[Henrik Bengtsson]

groups <- lapply(1:6, rep, each=4)
groups[[4]] <- groups[[4]][-1]  # Remove one from 4th group
groups <- unlist(groups)

/HB

On 2/19/07, James W. MacDonald <jmacdon at med.umich.edu> wrote:
> Ingrid H. G. Østensen wrote:
> > Hi
> >
> > Why is it [-14] and not [-15]? Is the group parameter zero based?
>
> Actually I was completely off. The third replicate of the fourth group
> would be the 12th member of the vector, so you want [-12]. Although any
> of [-10], [-11], [-12] would result in the same thing, as all you want
> to do is end up with a groups vector that looks like
>
> 1 1 1 2 2 2 3 3 3 4 4 5 5 5 6 6 6
>
> So removing any of the 4s will give you what you want.
>
> Sorry for the confusion.
>
> Best,
>
> Jim
>
>
> >
> > Regards,
> > Ingrid
> >
> >
> >
> >
> >
> > Hi Ingrid,
> >
> > Ingrid H. G. Østensen wrote:
> >
> >>Hi
> >>
> >>I have an experiment with 24 cel files divided into 6 groups (4 of
> >>each type). In affycoretools the group parameter would be like this:
> >>groups = rep(1:24, each = 4).
> >>
> >>After the QC I found out that one of the arrays was really bad and
> >>had to be removed. In other words there are now 5 groups with 4
> >>arrays and one with 3 arrays. What should I put in the group
> >>parameter now? I have tried different things but nothing has worked
> >>so far.
> >
> >
> > The groups argument (not a parameter) you are specifying isn't correct
> > to begin with. You want groups = rep(1:6, each = 4). The groups argument
> > you are specifying now is a numeric vector of length 96, instead of
> > length 24. I should probably put in some error checking to prevent
> > mis-specified groups arguments.
> >
> > Anyway, the groups argument just specifies what group each celfile
> > belongs to, so you can simply subset the correct argument to remove one
> > of the replicates for the group that has been reduced. For instance,
> > let's say you removed the third replicate of the fourth group. You can
> > then specify the groups argument like this:
> >
> > groups = rep(1:6, each=4)[-14]
> >
> > Best,
> >
> > Jim
> >
> >
> >
> >
> >>Regards, Ingrid
> >>
> >>
> >>
> >>
> >>[[alternative HTML version deleted]]
> >>
> >>_______________________________________________ Bioconductor mailing
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> >
> >
> >
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
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>
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