Displaying 20 results from an estimated 400 matches similar to: "Two way clustering"
2010 Jul 12
1
Extract Clusters from Biclust Object
Dear all,
I share the problem Linda Garcia and Ram Kumar Basnet described; I have a
biclust object, containing several clusters. For drawing a heatmap, it is
possible to specify the cluster to be plotted. However, I'd like to extract
the clusters in this manner:
Cond.1 Cond.2
Gene - value - value
just like drawHeatmap specifies each cluster. Is there a way to extract
single
2009 Jun 15
4
reading Excel file
Dear all,
I was using older version of R (installed early). I install new version of R (R.2.9.0) but i could not find package "xlsReadWrite" to read Excel file. Is there any alternatives to read Excel file ?
I hope it should be.
I need help although it is minor querry.
Thanks in advance.
Sincerely,
Ram Kumar Basnet
Wageningen University,
The Netherlands
[[alternative HTML
2003 Sep 03
1
Another R syntax question
The file src/library/base/R/print.R
contains this line:
x0 <- xm[okP]==0 != (as.numeric(Cf[okP])==0)
I didn't know R allowed that, and I wonder if it is deliberate?
In mathematics, you would expect x = y not= z to mean
(x = y) and (y not= z).;
In R, it is parsed as (x == y) != z.
While I have to admit that the spacing around == and != in
2012 Nov 21
6
Scaling values 0-255 -> -1 , 1 - how can this be done?
I have a dataframe in which I have values 0-255, I wish to transpose them such that:
if value > 127.5 value = 1
if value < 127.5 value = -1
I did something similar using the "binarize" function of the biclust package, this transforms my dataframe to 0 and 1 values, but I wish
to use -1 and 1 and looking for a way in R to do this.
Brian
2005 Jul 29
3
Error Downloading Matrix Package
I'm trying to update my Matrix package given the update last night. But
the following error is generated. I've tried restarting R and deleting
my old Matrix package. Can anyone suggest how this might be resolved?
> install.packages('Matrix')
trying URL
'http://www.ibiblio.org/pub/languages/R/CRAN/bin/windows/contrib/2.1/Mat
rix_0.98-1.zip'
Content type
2012 Nov 08
1
Package "glmulti": Include a variable in ALL models
Dear all,
I have a question about the glmulti package. I want to include some variables in all models. To that end I applied the wrapper function as shown in the examples (http://www.inside-r.org/packages/cran/glmulti/docs/glmulti).
To include the variable "Geslacht" in all models:
> glm.redefined = function(formula, data, always="", ...)
2003 Aug 15
3
How to reinstall rpart?
After entering ?library(rpart)?, I tried to plot an existing rpart tree, and
got this error message: Error: couldn't find function "plot.rpart".
However, ??plot.rpart? does bring up the help for the function. The same
things occur for text.rpart, although print(my.tree) does work.
So, I tried to re-install rpart using Packages | Install from CRAN, but
then I get this
2008 Nov 18
1
Statistical querry on Partial correlation test
Hi R users,
I want to calculate the partial correlation (first or second order) and their corresponding significance test (p-value).
I used
> library(corpcor)
and "cor2pcor" function to calculate partial correlation but could not calculate "p-value".
If some one knows the R package or function to calculate corresponding "p-value", It will be great help.
Thanks
2012 Nov 17
2
Using cbind to combine data frames and preserve header/names
I have a dataframe that has a header like so:
class value1 value2 value3
class is a factor
the actual values in the columns value1, value2 and value3 are 0-255, I wish to binarize these using biclust.
I can do this like so:
binarize(dataframe[,-1])
this will return a dataframe, but then I lose my first column class, so I thought I could combine it like so:
dataframe <-
2011 Nov 16
2
Conversion of symmetry matrix into a vector
Dear R users,
I am not good in R-language programming. So, i need your help.
I want to convert my lower-triangle value of symmetry matrix into a vector with their row and column name.
I found a function called "sm2vec" in "corpcor" package but it give only a vector of values but not row and column names. But i also want ROW and COLUMN name together with their corresponding
2004 Jul 15
1
lattice (PR#7093)
Full_Name: michael cole
Version: 1.9.1
OS: Windows
Submission from: (NULL) (80.219.153.13)
When trying to install lattice graphics... I receieve the following:
trying URL `http://cran.r-project.org/bin/windows/contrib/1.9/lattice_0.9-16.zip'
Content type `application/zip' length 496618 bytes
opened URL
downloaded 484Kb
package 'lattice' successfully unpacked and MD5 sums
2009 Apr 28
1
Cannot update.packages (error message)
When trying to update (various) packages using update.packages() I get the following error message for various packages
package 'fBasics' successfully unpacked and MD5 sums checked
Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
malformed bundle DESCRIPTION file, no Contains field
>
This happens with other packages besides fBasics (Matrix, as well as others) and I
2009 Apr 28
1
R-2.9.0 malformed bundle DESCRIPTION file, no Contains field
When trying to update (various) packages using update.packages() I get the following error message for various packages
package 'fBasics' successfully unpacked and MD5 sums checked Error in unpackPkg(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib) :
malformed bundle DESCRIPTION file, no Contains field
>
This happens with other packages besides fBasics (Matrix, as well as others)
2004 Apr 28
2
Problem in Installing Package from CRAN...
Hi,
I have installed R 1.9.0 under Windows XP. When I used
"Packages->Install Package(s) from CRAN..." to install the package 'gregmisc', I got this message:
> local({a <- CRAN.packages()
+ install.packages(select.list(a[,1],,TRUE), .libPaths()[1], available=a)})
trying URL `http://cran.r-project.org/bin/windows/contrib/1.9/PACKAGES'
Content type `text/plain;
2009 Nov 27
2
matching and extracting data
Dear all,
I have querry on how to extract the data by matching between two data set where one has the same elements multiple times?
For example, I have two matrix X and Y.
> X
[,1] [,2] [,3]
1 A 5 P
2 B 6 P
3 C 7 P
4 D 5 Q
5 E 6 Q
6 F 7 Q
7 G 5 R
8 H 6 R
9 I 7
2004 Aug 17
1
checkS3methods() change
Hi,
I'm using rw2000dev.exe (Win32) built on August 14.
If this isn't already planned, can I suggest that when
checkS3methods() (called by R CMD check) fails because of
a syntax error in a dependent package listed in the DESCRIPTION
file of the main package being checked, it would be nice if
checkS3methods() reported which dependent package caused it to
fail?
Running R CMD check on my
2008 Mar 07
2
Problems installing packages using the inbuilt facility: "Error i n gzfile(file, "r") : unable to open connection"
Hi
I have been trawling the web, FAQs, and R manuals for help on the following issue, but have failed and was wondering if anyone has a solution to the following problem:
After having installed R 2.6.2 for Windows (binary), I tried to install various packages. Every time I try loading a package (any package) via the built-in menu, I run into the following error message.
>
2008 Sep 15
1
how to plot PC2 vs PC 3 in PCA
Hi everybody,
I am doing principal component analysis (PCA) using "prcomp' function. When i did "Biplot", i did not found interesting result and it is based on Principal component (PC) 1 vs PC2. Now, i want to see"Biplot" in combination of either PC1 vs PC3 or PC2 vs PC 3. I did not get the ideas.
Does any one have ideas ?
I am optimistic on getting some idea.
2010 Dec 05
3
merging two vectors
Dear R users,
It may be very simple but it is being difficult for me.
I have two vectors with some common string. And, i want to combine into a vector in such a way that it includes string from both vectors and make a unique.
For example:
x <- paste(rep("A",5),1:5,sep = ".")
x
[1] "A.1" "A.2" "A.3" "A.4" "A.5"
y <-
2008 Dec 06
2
Barplot label
Dear all,
I am trying to make barplot from matrix with "beside=FALSE". I have 165 labels in my bar plot. When i plot the label horizontally below the barplot, then all labels are not appear in the plot due to lack of space. I used the following function:
barplot(t(bar), main="Barplot based on LCMS", ylab="RF membership Probability",