Dear all,
I have a programming problem with R, but in connection with arrays:
My goal is to extract just some columns (for which I have the label of
each) of an object of exprsSet type: the resulting object of the
expresso()
command from the affy package.
To be precise, let's say that I have 12 arrays, so my exprsSet object
is a
matrix of some thousands of lines by 12 columns.
My problem is that I don't have the rank of the columns I want to
extract,
but just the labels.
Let's say I have a matrix of 12 colums labelled "sample1" to
sample12". I
want to extract the columns labelled "sample1", sample4" and sample6",
which are non contiguous on my exprsSet matrix, in order to create a
new
matrix with these columns only.
I do not know how to obtain the indices (coordonates is maybe better?)
of
these 3 columns.
I think that when I will have these indices I will the be possible to
use
the subset() command ?
Does anyone could help me with this, because it seems I won't be able
to do
....
Thanks a lot for your help,
Florence.
In fact I just found out (one of) the way to do it, really sorry for
this
everybody.
I put there my command line if it can be useful for someone....
let's say you have the label(s) of the column(s) you want to extract
in a
variable called "ext", and that the exprSet object is called "eset" ,
I
think you can do you can do:
> extracted <- exprs(eset[, ext])
apologize again,
Florence.
>Dear all,
>
>I have a programming problem with R, but in connection with arrays:
>My goal is to extract just some columns (for which I have the label
of
>each) of an object of exprsSet type: the resulting object of the
>expresso() command from the affy package.
>
>To be precise, let's say that I have 12 arrays, so my exprsSet object
is a
>matrix of some thousands of lines by 12 columns.
>
>My problem is that I don't have the rank of the columns I want to
extract,
>but just the labels.
>Let's say I have a matrix of 12 colums labelled "sample1" to
sample12". I
>want to extract the columns labelled "sample1", sample4" and
sample6",
>which are non contiguous on my exprsSet matrix, in order to create a
new
>matrix with these columns only.
>
>I do not know how to obtain the indices (coordonates is maybe
better?) of
>these 3 columns.
>I think that when I will have these indices I will the be possible to
use
>the subset() command ?
>
>Does anyone could help me with this, because it seems I won't be able
to
>do ....
>
>Thanks a lot for your help,
>
>Florence.
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor@stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
In fact I just found out (one of) the way to do it, really sorry for
this
everybody.
I put there my command line if it can be useful for someone....
let's say you have the label(s) of the column(s) you want to extract
in a
variable called "ext", and that the exprSet object is called "eset" ,
I
think you can do you can do:
> extracted <- exprs(eset[, ext])
apologize again,
Florence.
>Dear all,
>
>I have a programming problem with R, but in connection with arrays:
>My goal is to extract just some columns (for which I have the label
of
>each) of an object of exprsSet type: the resulting object of the
>expresso() command from the affy package.
>
>To be precise, let's say that I have 12 arrays, so my exprsSet object
is a
>matrix of some thousands of lines by 12 columns.
>
>My problem is that I don't have the rank of the columns I want to
extract,
>but just the labels.
>Let's say I have a matrix of 12 colums labelled "sample1" to
sample12". I
>want to extract the columns labelled "sample1", sample4" and
sample6",
>which are non contiguous on my exprsSet matrix, in order to create a
new
>matrix with these columns only.
>
>I do not know how to obtain the indices (coordonates is maybe
better?) of
>these 3 columns.
>I think that when I will have these indices I will the be possible to
use
>the subset() command ?
>
>Does anyone could help me with this, because it seems I won't be able
to
>do ....
>
>Thanks a lot for your help,
>
>Florence.
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor@stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
Hi,
I have Linux Fedora 32 bit with 512 RAM
I would like to use Rgraphviz package.so, I did:
$ [root@localhost packages]# rpm -i
graphviz-1.12-1.i386.rpm
package graphviz-1.12-1 is already installed
[root@localhost packages]# R CMD INSTALL -l
/usr/local/lib/R/library Rgraphviz_1.4.0.tar.gz
---------------------------------------------
* Installing *source* package 'Rgraphviz' ...
** libs
gcc -I/usr/local/lib/R/include `dotneato-config
--cflags` -I/usr/local/include -D__NO_MATH_INLINES
-mieee-fp -Wall -fPIC -g -O2 -c Rgraphviz.c -o
Rgraphviz.o
In file included from
/usr/local/include/graphviz/render.h:45,
from common.h:21,
from Rgraphviz.c:1:
/usr/local/include/graphviz/macros.h:34:1: warning:
"NEW" redefined
In file included from common.h:13,
from Rgraphviz.c:1:
/usr/local/lib/R/include/Rdefines.h:129:1: warning:
this is the location of the previous definition
Rgraphviz.c: In function `Rgraphviz_agopen':
Rgraphviz.c:244: warning: implicit declaration of
function `GD_gvc'
Rgraphviz.c:244: error: invalid lvalue in assignment
make: *** [Rgraphviz.o] Error 1
ERROR: compilation failed for package 'Rgraphviz'
** Removing '/usr/local/lib/R/library/Rgraphviz'
-----------------------------------------------------
anyone has this before....?
thanks,
Saurin
On Thu, 23 Sep 2004, Saurin Jani wrote:
> Rgraphviz.c: In function `Rgraphviz_agopen':
> Rgraphviz.c:244: warning: implicit declaration of
> function `GD_gvc'
> Rgraphviz.c:244: error: invalid lvalue in assignment
> make: *** [Rgraphviz.o] Error 1
> ERROR: compilation failed for package 'Rgraphviz'
> ** Removing '/usr/local/lib/R/library/Rgraphviz'
> -----------------------------------------------------
> anyone has this before....?
First: Please quite CC'ing R-devel on these emails, I'm sure they
don't
really appreciate questions about Bioconductor packages there.
That being said, I'm fairly certain that you are picking up graphviz
headers that you don't think you're picking up as this is the first
time that you've got things setup in such a way that it actually
should
work ...
I know that in one of your offlist emails you had quite a lot of RPM
problems between, either from graphviz or from your system
administration
- did you manage to get those properly sorted out? This could quite
likely be the source of your problem.
Do you have the devel RPMs installed as well? this could also be it.
> Dear all,
>
> I have a programming problem with R, but in connection with arrays:
> My goal is to extract just some columns (for which I have the label
of
> each) of an object of exprsSet type: the resulting object of the
expresso()
> command from the affy package.
>
> To be precise, let's say that I have 12 arrays, so my exprsSet
object is a
> matrix of some thousands of lines by 12 columns.
>
> My problem is that I don't have the rank of the columns I want to
extract,
> but just the labels.
> Let's say I have a matrix of 12 colums labelled "sample1" to
sample12". I
> want to extract the columns labelled "sample1", sample4" and
sample6",
> which are non contiguous on my exprsSet matrix, in order to create a
new
> matrix with these columns only.
the exprSet structure is designed to make such operations extremely
simple. to illustrate, consider the example exprSet called eset
in Biobase
library(Biobase)
data(eset)
colnames(exprs(eset))
now you will see that the column names are the letters A-Z for
this example; in your case, they should be sample1-sample12 in some
arbitrary order
suppose I just want the columns "D", "H", "J":
eset2 <- eset[, c("D", "H", "J")]
eset2 is now the desired exprSet
[if for some reason your exprSet lacks column labels in the exprs
component, you can add them, but be sure to add the same labels
as the rownames(pData(yourEset))]
