R help - Feb 2006 - cor/group by???

Can someone help me calculate correlations for grouped values?

Heres what my first few line of data look like:
> head(cmexpr)
  LLID  GMID    CEXPR    MEXPR
1 1005 10831 2.057462 -0.08486
2 1005 10831 2.057515 -0.08486
3 1005 10831 2.057462  0.01209
4 1005 10831 2.057515  0.01209
5 1005 10836 2.050980  0.17237
6 1005 10836 2.018576  0.17237

LLID is gene id, GMID is cell line id, the EXPR columns are gene expression is
two different microarray experiments.

I'd like to get correlations for each gene id (1005, 1006, etc)

Heres what I've tried so far:

sapply(by(cmexpr[3:4],cmexpr$LLID, function(x) cor(cmexpr$CEXPR,cmexpr$MEXPR,
use = "pairwise.complete.obs")), function(x) x,simplify=T)

I think this is close to what I need, but its giving me the same corr for each
gene, which is not right:

       1005       10083       10146       10158       10174       10206
-0.04751543 -0.04751543 -0.04751543 -0.04751543 -0.04751543 -0.04751543
      10211       10212       10219       10363       10484       10492
-0.04751543 -0.04751543 -0.04751543 -0.04751543 -0.04751543 -0.04751543

Sorry if this sounds like a newbie question; it seems like it ought to be pretty
straightforward, but I've wrestled with both the R documenation and mailing
list archive and can't seem to get it right.

Thanks

B



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bin999 at lycos.com writes:
> Can someone help me calculate correlations for grouped values?
> 
> Heres what my first few line of data look like:
> 
> > head(cmexpr)
>   LLID  GMID    CEXPR    MEXPR
> 1 1005 10831 2.057462 -0.08486
> 2 1005 10831 2.057515 -0.08486
> 3 1005 10831 2.057462  0.01209
> 4 1005 10831 2.057515  0.01209
> 5 1005 10836 2.050980  0.17237
> 6 1005 10836 2.018576  0.17237
> 
> LLID is gene id, GMID is cell line id, the EXPR columns are gene expression
is two different microarray experiments.
> 
> I'd like to get correlations for each gene id (1005, 1006, etc)
> 
> Heres what I've tried so far:
> 
> sapply(by(cmexpr[3:4],cmexpr$LLID, function(x)
cor(cmexpr$CEXPR,cmexpr$MEXPR, use = "pairwise.complete.obs")),
function(x) x,simplify=T)
> 
> I think this is close to what I need, but its giving me the same corr for
each gene, which is not right:
> 
>        1005       10083       10146       10158       10174       10206
> -0.04751543 -0.04751543 -0.04751543 -0.04751543 -0.04751543 -0.04751543
>       10211       10212       10219       10363       10484       10492
> -0.04751543 -0.04751543 -0.04751543 -0.04751543 -0.04751543 -0.04751543
> 
> Sorry if this sounds like a newbie question; it seems like it ought to be
pretty straightforward, but I've wrestled with both the R documenation and
mailing list archive and can't seem to get it right.
You're passing a function to by() whose result does not depend
on the argument x ...

This might be clearer:

c(by(cmexpr, cmexpr$LLID, with, cor(CEXPR, MEXPR, use="pair")))

or

sapply(split(cmexpr, cmexpr$LLID), with, cor(CEXPR, MEXPR,
use="pair"))

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