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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

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.

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 <-

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",   

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

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   [[alternative HTML

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")

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   [[alternative

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

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   [[alternative HTML version deleted]]

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 guess this is right package

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 Kumar Basnet, Wageningen University. [[alternative HTML version deleted]]

I have very large data set. I want to make subset of data based on the matching. For example,   > x [1] "a" "b" "c" "f" > yy                                                                     "a" "-0.761988113636315" "-0.117672628171555" "-0.885641151614679" "b" "-1.13288279283289" 

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  

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 new R user and could not understand what is the problem and also don't know the easiet

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 similarly, X1, X2.......X5 in case of Var2, only X1 in case of Var3 and none of the predictors in case

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 "Day" is time-variable   ## my response variable   rl <-

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.numeric(vio),lambda=0.5,normalize=FALSE,intercept=TRUE) Error in one %*% x : requires numeric

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

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 "Day" is time-variable my response variable rl <-