correlating rows of two differently-sized data frames in R

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

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

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 at 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 at 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



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