On 12/2/2010 11:36 AM, David Winsemius wrote:
On Dec 2, 2010, at 5:22 AM, Karl Brand wrote:
Cheers Bill.
You got me halfway, since:
> temp <- merge(x=x, y=y[,17, drop=FALSE], by="rownames", sort=FALSE)
Error in fix.by(by.x, x) : 'by' must specify valid column(s)
but, using "row.names" instead of "rownames", like:
> temp <- merge(x=x, y=y[,17, drop=FALSE], by="row.names", sort=FALSE)
works (but adds a column "Row.names").
Which seems some what counter intuitive to me since i am feeding in
two matrices to the merge function, which i understand have
'rownames', not 'row.names' as data frames have, right? Although the
output of merge() is a data frame...
This reminds me of physicists using high energy particles to investigate
the structure of the nucleus. But you have alternatives to what might be
called "destructive debugging through binoculars". Instead of throwing
code at your data and asking the assembled audience of soothsayers to
tell you what went wrong by examining the debris, why don't you show us
what the data objects actually look like?
Ofcourse David, sorry- my lazy.
Is str() enough to put away the binoculuars and maybe highlight the
source of my ignorance?
> str(x)
num [1:140, 1:7] 4.93e-02 2.83e-02 1.07e-02 2.68e-02 3.92e-05 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:140] "1415743_at" "1415887_at" "1416332_at"
"1416340_a_at" ...
..$ : chr [1:7] "R.S.adj.pvalue" "R.S.Tau" "R.S.xpiek" "R.S.xdal" ...
> str(y)
num [1:140, 1:18] 0.573 1 0.752 0.768 0.399 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:140] "1427982_s_at" "1430520_at" "1454086_a_at"
"1419652_s_at" ...
..$ : chr [1:18] "R.S.1" "R.S.2" "R.S.3" "R.S.4" ...
> source(.trPaths[5], echo=TRUE, max.deparse.length=150)
> str(temp)
'data.frame': 140 obs. of 9 variables:
$ Row.names :Class 'AsIs' chr [1:140] "1415743_at" "1415887_at"
"1416332_at" "1416340_a_at" ...
$ R.S.adj.pvalue: num 4.93e-02 2.83e-02 1.07e-02 2.68e-02 3.92e-05 ...
$ R.S.Tau : num 21.6 23.6 26.6 29.7 18.8 20 24.6 27.9 23.9 22.7 ...
$ R.S.xpiek : num 6.74 17.46 15.81 15.39 14.73 ...
$ R.S.xdal : num 16.94 1.76 22.8 1.12 5.41 ...
$ R.S.p1 : num 0.0004 0.0001 0.0467 0.0024 0 ...
$ R.S.p2 : num 0.0039 0 0.002 0.019 0.0001 0.0035 0.0351
0.0126 0.0028 0.0192 ...
$ R.S.p3 : num 0.0178 0.0004 0.0101 0.0312 0.0012 0.022 0.0008
0.0151 0.0048 0.0317 ...
$ V1 : num 3.96 -0.94 1.04 1.94 -2.53 ...
>
--
Karl Brand <k.br...@erasmusmc.nl>
Department of Genetics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
P +31 (0)10 704 3211 | F +31 (0)10 704 4743 | M +31 (0)642 777 268
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