[R] difficulties in pvclust package

Hi I am a new user of R, and doing clustering analysis (dendrogram). I am quite interested in pvclust package because of facility of AU probability of each cluster. Now, i have a problem when handling large data set. I have data set of 183 rows and 5546 columns, and interested to make clusterin

[R] 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   Sinc

Re: [R] how to increase row number

ROTECTED] Cc: r-help@r-project.org Date: Tuesday, September 2, 2008, 9:43 AM On 9/2/2008 12:30 PM, ram basnet wrote: > 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

[R] error in Elastic net

Dear R users,   I am new user for elastic net. I am trying to use elasticnet library. I have marker data with 359 markers and 168 samples, and response is metabolites. I am trying to do regression between a metabolite and markers.  But i am getting the following error:   > en<-enet(marker,as.numer

[R] Error in elastic net

Dear R users,   I am new user for elastic net. I am trying to use elasticnet library. I have marker data with 359 markers and 168 samples, and response is metabolites. I am trying to do regression between a metabolite and markers.  But i am getting the following error:   > en<-enet(marker

[R] missing value in Elastic Net

Dear R users,    Does Elasticnet (package "elasticnet") handle the missing value in predictors ? If some one can provide the way to hadle missing value, it will great. Thanks in advance.   Sincerely, Ram Kumar Basnet Wageningen University, The Netherlands   [[alternative HTML ver

[R] 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.    

[R] 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   

[R] Type III sum of square in ANOVA

Dear all,   Does some body have idea on how to extract Type III sum of Square from "lm" or "aov" function in R ? I could not figure out it.   If this is minor and irrelevant to post in this mail, I am sorry for that. Thanks.     Sincerely, Ram Kumar Basnet Wageningen University, Netherlands  

[R] 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.   Sinc

[R] selecting significant predictors from ANOVA result

Dear all,   I did ANOVA for many response variables (Var1, Var2, Var75000), and i got the result of p-value like below. Now, I want to select those predictors, which have pvalue less than or equal to 0.05 for each response variable. For example, X1, X2, X3, X4, X5 and X6 in case of Var1, and

Re: [R] selecting significant predictors from ANOVA result

wrote: From: Bert Gunter Subject: RE: [R] selecting significant predictors from ANOVA result To: "'ram basnet'" , "'R help'" Date: Wednesday, January 27, 2010, 7:56 AM Ram: You do not say how many cases (rows in your dataset) you have, but I suspect

[R] 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

[R] problem in asreml function in wgaim package

Dear R users,   I am trying to use "wgaim" package for QTL analysis using mixed model approach. But i am stuck with "asreml" function while using "wgaim" package. Do i need a separate package to activate "asreml" function beside "wgaim" package ?   If so, i tried to download "Asreml-R" package (i

Re: [R] problem in asreml function in wgaim package

Dear Uwe Ligges,   Thanks for your prompt response. I visited website link that you mentioned. It seems it needs license though it is R package. Am i correct ?   Thanks   Regards,   Ram Kumar Basnet   From: Uwe Ligges To: ram basnet Cc: R help Sent: Friday, August 12, 2011 7:13 PM Subject: Re

Re: [R] problem in asreml function in wgaim package

Dear Uwe Ligges, Thanks for response. I mean this R package is not free package.   Thanks   Ram Kumar Basnet   From: Uwe Ligges To: ram basnet Cc: R help Sent: Friday, August 12, 2011 7:28 PM Subject: Re: [R] problem in asreml function in wgaim package On 12.08.2011 19:21, ram basnet wrote

[R] 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 col

Re: [R] Conversion of symmetry matrix into a vector ONE MORE QUESTION

Dear Michael,   Thank you very much.   Ram     From: R. Michael Weylandt Sent: Wednesday, November 16, 2011 1:48 PM Subject: Re: [R] Conversion of symmetry matrix into a vector ONE MORE QUESTION Try the as.dist() function -- it won't change any values, only giv

[R] Problem in Fitting model equation in "nls" function

Dear R users,   I am struggling to fit expo-linear equation to my data using "nls" function. I am always getting error message as i highlighted below in yellow color:     ### Theexpo-linear equation which i am interested to fit my data:   response_variable =  (c/r)*log(1+exp(r*(Day-tt))), w

[R] Problem in fitting model equation in "nls" function

Dear R users, I am struggling to fit expo-linear equation to my data using "nls" function. I am always getting error message as i highlighted below in yellow color: ### Theexpo-linear equation which i am interested to fit my data:   response_variable =  (c/r)*log(1+exp(r*(Day-tt))), wher

[R] problem in fitting model in NLS function

Dear R users, I am struggling to fit expo-linear equation to my data using "nls" function. I am always getting error message as i highlighted below in yellow color:  Theexpo-linear equation which i am interested to fit my data:   response_variable =  (c/r)*log(1+exp(r*(Day-tt))), where "

[R] Error: can not allocate vector of 117.3 Mb

Hi R users,   I am doing multiscale bootstrapping for clustering through pvclust package. I have large data set (observations 182 and variables 5546). When i tried to make bootstrapping, then i got message as "Bootstrap (r = 0.5)Error: cannot allocate vector of size 117.3 Mb". I am n

[R] Two way clustering

Hi R users,   I am trying to do two-way clustering (using information of both observation and variables). Is there any package available in R. Another querry, if somebody can provide related information (website) regarding this statistics, it will be great. Thanks in advance.   Regards,   Ram Ku

[R] Querry in Biclust

Dear R users,   I am new user of R as well as Biclust package. I am handling data set of (236 genes and 166 conditions) and i knew the importance of Biclustering. Now, I am able to get some results but can not understand the result as what i am thinking. My thinking may be wrong. I used followin

[R] how to make subset of large data

8017"  "0.97145488124429"   "-0.591375965267432" "e" "-0.81749699489" "0.598589864959733"  "-0.74697501001117"  "f" "-1.59120505480671"  "-1.67283394866541"  "0

[R] 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

[R] 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

[R] 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

Re: [R] Can't load Rgraphviz on windows-based R

Dear all, I am facing the same problem. I followed the all instructions given in help file and some steps of previous discussion (from google search) but I could not install package Rgraphiviz in windows.  I tried even the instructions given to install Bioconductor package then only able to inst

[R] 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 L