HI Michael,

sorry, didn't mean to hit "reply" rather than "reply all".  Thanks for your
advice, will try that!

Jen

On Thu, Aug 9, 2012 at 6:57 PM, R. Michael Weylandt <
michael.weylandt@gmail.com> wrote:

> Hi Jen,
>
> It's generally best to keep cc'ing R-help so others can lend a hind
> when I step away from my computer:
>
> On Thu, Aug 9, 2012 at 11:49 AM, Jennifer Hobbs <jenachobbs@gmail.com>
> wrote:
> > Hi Michael -
> >
> > thanks for the advice - I did find merge() just after posting but I'm
> having
> > difficulty with using it.  I've loaded both datasets; then I tried
> >
> >> CombinedData<-merge(MethyData1,ExprData1)
> >
> > but when I looked at CombinedData, I found there was no actual data in
> it:
> >
> >> str(CombinedData)
> > 'data.frame': 0 obs. of  20 variables
>
> Take a look at
>
> ?merge.data.frame
>
> in particular since there are many different forms of merges. Your
> original post suggests you may want to set
>
> all = TRUE
> by = "Location"
>
> Hope that helps,
> Michael
>
>
>
> >
> > I thought this might be due to the fact that my column names, as well as
> the
> > row names, in both data sets were the same, so I renamed the column
> names in
> > ExprData1 and tried again:
> >
> >> colnames(ExprData1)<-NewExprNames
> >> merge(ExprData1,MethyData1)
> > Error: cannot allocate vector of size 4.2 Gb
> > In addition: Warning messages:
> > 1: In expand.grid(seq_len(nx), seq_len(ny)) :
> >   Reached total allocation of 8055Mb: see help(memory.size)
> > 2: In expand.grid(seq_len(nx), seq_len(ny)) :
> >   Reached total allocation of 8055Mb: see help(memory.size)
> > 3: In expand.grid(seq_len(nx), seq_len(ny)) :
> >   Reached total allocation of 8055Mb: see help(memory.size)
> > 4: In expand.grid(seq_len(nx), seq_len(ny)) :
> >   Reached total allocation of 8055Mb: see help(memory.size)
> >
> > I was surprised about this, as I'm using a 64-bit computer and it's
> managed
>
> You'll also need to be using a 64 bit build of R. Merging is pretty
> memory expensive so if you're right on the edge of what R can handle
> you might have to look into a more specialized solution (such as an
> SQL backend)
>
> > to deal with much larger data sets before now (I know that's not the only
> > criterion, but my understanding of computers isn't extensive).  I had
> > previously run up against a memory problem because I hadn't transformed
> my
> > data (I thought I was looking at columns, the computer was looking at
> rows)
> > so I tried transforming both data sets and merging again, but I end up
> with
> > another empty data frame:
> >
> >> tED1<-t(ExprData1)
> >> tMD1<-t(MethyData1)
> >> CombineData<-merge(tED1,tMD1)
> >> str(CombineData)
> > 'data.frame': 0 obs. of  152247 variables:
> >
> > This is where I'm stuck.  Any advice would be hugely appreciated!
> >
> > Jen
> >
> > On Thu, Aug 9, 2012 at 5:28 PM, R. Michael Weylandt
> > <michael.weylandt@gmail.com> wrote:
> >>
> >> Perhaps load them both and ?merge can show you the way.
> >>
> >> Michael
> >>
> >> On Thu, Aug 9, 2012 at 9:54 AM, JenniferH <jenachobbs@gmail.com> wrote:
> >> > Hello everyone,
> >> >
> >> > I have two sets of data, with the following structure:
> >> >
> >> > DataSet1
> >> > Location   Part    Sample 1   Sample 2
> >> > A                     1           value         value
> >> > A                     2           value         value
> >> > A                     3           value         value
> >> > B                     1           value         value
> >> >
> >> > DataSet2
> >> > Location   Sample 1    Sample 2
> >> > A                      value          value
> >> > B                      value          value
> >> > C                      value          value
> >> >
> >> > I would like to look at the correlations between DataSet1 and
> DataSet2,
> >> > such
> >> > that each row in Location A from DataSet1 is paired with the Location
> A
> >> > row
> >> > from DataSet2, and so forth.  So far, my only ideas  involve trying to
> >> > copy-paste each of the rows in DataSet2 the number of times each
> occurs
> >> > in
> >> > DataSet1 on a spreadsheet before loading the sets into R; however, as
> I
> >> > have
> >> > approaching 8000 rows in DataSet2, this is clearly not a workable
> >> > solution!
> >> >
> >> > I'm sure there's a simple solution to this, so I'm sorry if this seems
> >> > like
> >> > a really silly question.
> >> >
> >> > Thanks for your help!
> >> >
> >> > Jen
> >> >
> >> >
> >> >
> >> > --
> >> > View this message in context:
> >> >
> http://r.789695.n4.nabble.com/correlating-rows-of-two-differently-sized-data-frames-in-R-tp4639774.html
> >> > Sent from the R help mailing list archive at Nabble.com.
> >> >
> >> > ______________________________________________
> >> > R-help@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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