similar to: DESeq2 pairwise compasion

Hi , I am trying to open vignette DESeq2 but getting below error: > vignette("DESeq2") > START /usr/bin/evince "/usr/lib64/R/library/DESeq2/doc/DESeq2.pdf" Cannot parse arguments: Cannot open display: xdg-open: no method available for opening '/usr/lib64/R/library/DESeq2/doc/DESeq2.pdf' -- *Yogesh Gupta* *Postdoctoral Researcher* *Department of Biological

I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames) >

Dear All, I am trying to make dendogram based on gene expression matrix , but getting some error: I countMatrix = read.table("count.row.txt",header=T,sep='\t',check.names=F) colnames(countMatrix) count_matrix <- countMatrix[,-1] # remove first column (gene names) rownames(count_matrix) <- countMatrix[,1] #added first column gene names as rownames)

Thanks for all your great answers. The app I?m working on is indeed an exploratory data analysis tool for gene expression, which requires a bunch of bioconductor packages. I guess for now, my best solution is to divide my app into modules and load/unload packages as the user switch from one module to another. This brought me another question: it seems that unload package with the

On 04/05/2016 08:44, Martin Maechler wrote: >>>>>> Qin Zhu <qinzhu at outlook.com> >>>>>> on Mon, 2 May 2016 16:19:44 -0400 writes: > > > Hi, > > I?m working on a Shiny app for statistical analysis. I ran into this "maximal number of DLLs reached" issue recently because my app requires importing many other packages.

On 05/04/2016 05:15 AM, Prof Brian Ripley wrote: > On 04/05/2016 08:44, Martin Maechler wrote: >>>>>>> Qin Zhu <qinzhu at outlook.com> >>>>>>> on Mon, 2 May 2016 16:19:44 -0400 writes: >> >> > Hi, >> > I?m working on a Shiny app for statistical analysis. I ran into >> this "maximal number of DLLs

>>>>> Qin Zhu <qinzhu at outlook.com> >>>>> on Fri, 6 May 2016 11:33:37 -0400 writes: > Thanks for all your great answers. > The app I?m working on is indeed an exploratory data analysis tool for gene expression, which requires a bunch of bioconductor packages. > I guess for now, my best solution is to divide my app into modules and

Hello, I'm trying to fetch a data frame through the C API, and have no problem doing this when all columns are numbers, but when there is a column of strings I have a problem. On the C-side the function looks like: SEXP myfunc(SEXP df), and it is called with a dataframe from the R side with: .Call("myfunc", somedataframe) On the C side (actually C++ side) I use code like this:

Hello R-devel, I am currently attempting to implement an API similar to data.table wherein single bracket subsetting can accept an unquoted expression to be evaluated in the context of my object. A simple example from the data.table package looks like this: DT <- data.table(col1 = c('a', 'b', 'c'), col2 = c('x', 'y', 'z')) DT[col1 ==

Hi, directory<- "/home/arunksa111/data.new" #first function filelist<-function(directory,number,list1){ setwd(directory) filelist1<-dir(directory) direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""), full.names = FALSE, recursive = TRUE) list1<-lapply(direct, function(x) read.table(x,header=TRUE, sep =

Hi Michael, Here is the result of my first testing: (0) Dr. Watson Sorry, I should have given a more precise description: by default in R exists a function with the name 'table', if you use this name as in odbcPrimaryKeys(0, table) a Dr. Watson occurs, because table does not give a table name. However, it is always a good idea to prevent Dr. Watsons, even if it is triggered by a

Hello, All: The vignette with the sos package used "upquote.sty", required for R Journal when it was published in 2009. Current CRAN policy disallows "upquote.sty", and I've so far not found a way to pass "R CMD check" with sos without upquote.sty. I changed sos.Rnw per an email exchange with Prof. Ripley without solving the problem; see below. The

Hello, I have RNAseq data, which I am trying to analyze with DESeq. My file (tab delimited .txt) appears to be correct: >head(myfile) VZ_w13 VZ_w14a VZ_w14b VZ_w15a VZ_w15b VZ_w16a ENSG00000253101 0 0 0 0 0 0 ENSG00000223972 0 0 0 0 0 0... However, when I try to analyze the data with >cds <-

Hello all, I have a data file table.txt which i have attached. I am trying to pass the columns as arguments to a function "totnorm" where i am displaying a total normalization plot. The function is given below: totnorm<-function(x,y){scale<-sum(x)/sum(y);xlab<-colnames(x);ylab<-colnames(y);x1<-x[[1]];y1<-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6, col.lab=4);}

Hello all, I have a data file table.txt which i have attached. I am trying to pass the columns as arguments to a function "totnorm" where i am displaying a total normalization plot. The function is given below: totnorm<-function(x,y){scale<-sum(x)/sum(y);xlab<-colnames(x);ylab<-colnames(y);x1<-x[[1]];y1<-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6, col.lab=4);}

Library gmodels include a function CrossTable that is useful for crosstabulation. In the help, it is indicated that one can call this function as CrossTable(data), were data is a matrix. However, when I try to use this option, it doesn't help. Any idea? Is there a bug? Thanks for your help. Prof. Albert Sorribas Grup de Biomatem?tica i Bioestad?stica Departament de Ci?ncies M?diques B?siques

Dear All, Using RODBC I have read in a (429 x 11) dataframe from Access, and would like to append two columns of transformed data (429 x 2) to the original table (thereby making it a 429 x 13 table). I would ideally like this to be the same name etc as the original table in Access. I have used the following command: R>

Hello R users, Doing My PhD I collected count data which I believe is zero inflated. I have run a statistical model with lmer and family=poisson and got summary(model)@sigma=1 so I believe there is no overdispertion. I would like to use the fmr function from the 'gnlm' library but I just cannot figure out from the examples in the help page and some forums out there how to convert the lmer

i have a data frame(dat) which has many variables.and i use the following script to get the crosstable. >danx2<-c("x1.1","x1.2","x1.3","x1.4","x1.5","x2","x4","x5","x6","x7","x8.1","x8.2","x8.3","x8.4","x11",

Dear R users, I have a follow-up question on sqlSave(). Since most of the output from the tests I use are lists, I would like to loop to export each element of the list and append it to the sheet. Here is what I do: > library(RODBC) > test <- structure(list(m = structure(c(0.090909090909091, 0.181818181818182, 0.272727272727273, 0.363636363636364, 0.454545454545455,