[R] How to pool a group of samples and take the ave.

affy snp affysnp at gmail.com
Mon Nov 12 21:48:50 CET 2007


Thanks Jim and Ben.

Allen

On Nov 12, 2007 3:43 PM, Benilton Carvalho <bcarvalh at jhsph.edu> wrote:
> it's defined in Biobase.
>
>
> On Nov 12, 2007, at 3:30 PM, affy snp wrote:
>
> > Thanks Jim. It is way simple. Great.
> > Is there any function like rowMedians() which
> > could take the median value across samples?
> >
> > Allen
> >
> > On Nov 12, 2007 3:10 PM, jim holtman <jholtman at gmail.com> wrote:
> >> Try something like this:
> >>
> >> myAvg <- rowMeans(A[,48:243])
> >> B <- A[1:47,] / myAvg
> >>
> >>
> >> On Nov 12, 2007 1:37 PM, affy snp <affysnp at gmail.com> wrote:
> >>> Dear list,
> >>>
> >>> Hi! I have a table A, 238304 rows and 243 columns (representing
> >>> samples). First of all, I would like to pool a group of samples
> >>> from 48th column to 243rd column and take the average across
> >>> them and make a single column,saying as the reference column.
> >>>
> >>> Second, I want to use each column of first 47 columns in table
> >>> A divided by the reference column and end up with a new table
> >>> B with 238304 rows and 47 columns.
> >>>
> >>> Is there any simple code which especially could do sth like
> >>>       reference_column<-(A[,48]+A[,49]+...A[,243])/196
> >>> and B<-A[,1:47]/reference_column?
> >>>
> >>> Thank you very much for your help!
> >>>
> >>> Best,
> >>>      Allen
> >>>
> >>> ______________________________________________
> >>> R-help at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>> PLEASE do read the posting guide
> >>> http://www.R-project.org/posting-guide.html
> >>> and provide commented, minimal, self-contained, reproducible code.
> >>>
> >>
> >>
> >>
> >> --
> >> Jim Holtman
> >> Cincinnati, OH
> >> +1 513 646 9390
> >>
> >> What is the problem you are trying to solve?
> >>
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>



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