Displaying 20 results from an estimated 900 matches similar to: "Error: can not allocate vector of 117.3 Mb"
2008 Oct 01
1
Error: cannot allocate vector of size 117.3 Mb
Dear R users,
I am using RandomForest package. While using this package, i got
"Error: cannot allocate vector of size 117.3 Mb" .........................message.
I had this problem earlier too but could not manage. Is there any way to solve this problem or to increase vector size ? My data set is of 163 samples and 5546 variables.
I tried through "? Memory" function to solve
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
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
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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",
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.
2008 Oct 27
3
Problem in installation of "Rgraphviz" package
Dear R users,
I am not so used to this R software. I have to use the package " Rgraphviz" but found some problem in the installation process. I download this package and store in R library but i am not getting this package in R installation list.
I made review in google search net and use the following command:
###
source("http://bioconductor.org/biocLite.R")
2008 Sep 02
1
how to increase row number
Hi
I think this may be simple task but creating trouble to me.
In my calculation, i have got large number of rows (5546) and column 182 but i am not able to see all the rows. May be somebody have idea how i can see all the rows ? I will be greatful if any body help me.
Thanks in advance
Sincerely,
Ram Kumar Basnet
Graduate student
Wageningen University
Netherlands
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2009 Nov 25
4
Importing many files from a single code
Dear R users,
Does somebody know the way to import many files by a single command in R ? I have 50 files in a directory and now, i am importing the files repeatedly (one by one). If there is a way to import all files at a time, it makes much more easy and save times too.
Thanks in advance.
Sincerely,
Ram Kumar Basent
Wageningen University,
the Netherlands
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2012 Jun 07
1
select subrows based on a specific column in a matrix
Hi all,
I have a matrix with 10000 rows and 10 columns. The last columns contains another identifiers but the values are not uniques so that I want to generate another matrix with rows with unique values in the last column.
If I did
tmp<-unique(my_mat$col10)
this will give me 8560 unique entries so the ideal matrix will be 8560X10 columns now then.
I tried
sub_mat<-my_mat[tmp,]
but
2010 Jul 20
1
p-values pvclust maximum distance measure
Hi,
I am new to clustering and was wondering why pvclust using "maximum"
as distance measure nearly always results in p-values above 95%.
I wrote an example programme which demonstrates this effect. I
uploaded a PDF showing the results
Here is the code which produces the PDF file:
-------------------------------------------------------------------------------------
s <-
2012 Jun 28
1
Merging listed dataset into one
Hello,
I'm wondering how I can merge two featuresets into one.
My dataset is two sets of microarray data and it looks like followings:
> rawData
$v1
TilingFeatureSet (storageMode: lockedEnvironment)
assayData: 2197815 features, 59 samples
element names: channel1, channel2
protocolData
rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ...
LT003990RU_D1_2010-11-04 (59
2010 Feb 02
2
hvcluster() with distance method from vegdist(), package = vegan
hello,
i'd be happy if someone could provide help with the following problem:
i have a dist.matrix that comes from vegdist() function of the vegan
package. the used method = "horn" is not accepted as argument in
hvcluster(...,dist.method="...").
is there a way to incorporate the method "horn" in hvcluster()?
thanks in advance!
yours,
kay
--
View this
2010 Aug 10
2
p-values with pvclust
Hi,
if you look at the first image (Image1) you see that there are 2 main
clusters 7 and 8
I wanted to use pvclust to calculate a p-value whether these clusters are
due to chance
or statistically significant. Unfortunately pvclust does not provide a
p-value for the first
brunch (7 and 8).
So I added a row to my matrix which is very different to the rest of the
data to create an additional
2011 Mar 05
1
pvclust crashing R on Ubuntu 10.10
Hi all
I am writing to you with a question regarding the pvclust package. And
yes, before the usual people produce their usual
contact-the-package-maintainers line, ye, I tried that but the emails
one can find on the web either bounce or are not responded to. Also,
yes, this error has already been reported as a bug but been shot down
as not reproducible
2006 Jul 10
2
pvclust missing values problem
Hello all,
I posted a question to this list last week and received no response. I am unsure if this means no-one knows the answer or if I posed the question badly. I'm going to assume I posed the question badly and try again. I am new to R so it is quite likely it's a very naive question, however if there is something blindingly obvious that I am missing or if there is another resource I
2013 Apr 19
5
how to subtotal by rows
Dear R-users,
I have a dataset as like below, and I want to subtotal the values of rice,wheat and maize by year for each fid.
fid year rice wheat maize
------------------------------------------------
1 1995 5 NA NA
1 1995 NA 3 NA
1 1995 NA NA 2
1 1996 4 NA NA
1
2007 Jun 08
2
How to do clustering
Dear List,
I have another question to bother you about how to do clustering.
My data consists of 49 columns (49 variables) and 238804 rows.
I would like to do hierarchical clustering (unsupervised clustering
and PCA). So far I tried pvclust (www.is.titech.ac.jp/~shimo/prog/*pvclust*
/)
but I always had the problem like for R like "cannot allocate the memory".
I am curious about what
2010 Aug 09
1
(no subject)
Hi there,
I have been trying to use the "pvclust" package but have been having
some difficulties. This is the first time I have used R so I am sure the
mistake I am making is a basic one. The data I have is a distance matrix
and I have been using the command; fit <- pvclust(cluster, nboot=1000,
method.dist="euclidean") to try and perform hierarchical clustering with
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