The standard practice in Bioconductor with expression data is to manage the
information on expression plus information on samples in a unified way in
an ExpressionSet.  This has many benefits.  Were you to do this, you could
get chromosome-specific limitation of expression data in various ways.

If the data are from a well-annotated chip family, with a standard .db
annotation package, say chp.db, you could do, e.g.,

X9 = X[ get("9", revmap(chpCHR)), ]  # use an appropriate chromosome
identifier for the package

and all the sample information would propagate.  If you were not so lucky,
but still used expression set structure, you could
put the chromosome information in the featureData component, and use

X9 = X[ fData(X)$chrom == "9", ]

On Mon, Nov 28, 2011 at 9:30 AM, Assa Yeroslaviz <frymor@gmail.com> wrote:

> Hi everybody
>
> I would like to know if there is a way for sub-setting big data.frame of
> different chromosomes into separate data.frames for the specific
> chromosomes.
>
> I have the results of a microarray experiment in one huge excel sheet. one
> of the columns is df$Chromosomes
> I know I can sub-set it using
> for example:
> data_9=subset(data,Chromosome=="9")
> But I would like to know (probably for the next analysis) if there is a way
> of automating it. Can I, with one command separate my big file into 24
> separate data frames (chromosomes 1-22, X,Y)?
>
> Thanks
> Assa
>
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