similar to: Antwort: FW: R loops

hello everybody, I have a directory with over 3000 files with different names. I would like to make some vectors with the file names which are belong together. I'm trying to do it with a for loop in R: SF <- c("ad", "cd", "cer", "stress", "salty", "PC", "high", "transfer", "cold",

I was trying to install R on a unix server. Because of a firewall i can't install biocLite for working with Bioconductor. With windows it wasn't a problem. I used the option '--internet2' to bypass the firewall. I don't have any idea, how to do it with unix. I tried to set my proxy >Sys.putenv("http_proxy"="http...:8080")

Hello, Is it possible to change the default repositories? I've already changed the list in the repositories file under etc/ this is how my repositories file under R/etc looks like: row name menu_name URL default source win.binary mac.binary CRAN CRAN @CRAN@ TRUE TRUE TRUE TRUE BioC Bioconductor http://www.bioconductor.org TRUE TRUE TRUE FALSE

Hey, As a beginner to the limma package I tried to understand how to define a design matrix. I did both experiment examples in the "Limma user's Guide" manual. Afterwards I wanted to do it with my own data. Here I encounter a few problems. As an example I used four Control samples and 4 treated samples. 1. This is how my target files looks like: filename treated time.h

Hi, at the moment I'm trying to understand the limma/affy Packages. I've tried every example I could find to try and understand the ways to create design and contrast matrices. I must admit though, that I can't figure it out. I did a few times the estrogen files from the book "bioinformatics and computational biology solutions using R and Bioconductor". I know it's a

Hi all, I'm trying my best in changing the names of my experiments in the spectral map. My experiments are from six different time points, two as control and two treated experiments. I set have for each time point a different color . Now I want to change the symbols so that I have for the treated experiments one and for the controls a different one. But I want only two different symbols

Hi, I would like to substitute a semicolon with two double quotation marks and a comma inbetween. It suppose to look like that: I have: FBpp0070086;FBpp0099643;FBpp0112915 I would like to have: "FBpp0070086","FBpp0099643","FBpp0112915" I tried with various numbers of backslashes, but noe have worked. for example: gsub(";", "\\\",\"",

Hello everyone, I have a matrix of over 40000 line and about 30 columns. For my analysis I would like to add another column with ascending numbers (column header should be "order", and than 1,2,3,4 ....the end of the matrix). During my analysis I reorder them ( due to merge commands by a different column). How do I add such a column in an ascending order (or descending for what it

Hello R users, I'm trying to extract random samples from a big array I have. I have a data frame of over 40k lines and would like to produce around 50 random sample of around 200 lines each from this array. this is the matrix ID xxx_1c xxx__2c xxx__3c xxx__4c xxx__5T xxx__6T xxx__7T xxx__8T yyy_1c yyy_1c _2c 1 A_512 2.150295 2.681759 2.177138 2.142790 2.115344 2.013047

Hello, I'm trying to paste two columns of a matrix GB_ACC GENE GENE_SYMBOL NM_010657 NM_010657 NM_027162 NM_027162 NM_198863 NM_198863 NM_010727 NM_010727 These two column are a part of a 41,000 x 26 matrix. I wanted these two column to be pasted into one (the firstone, GB_ACC). I tried to do it with a for loop, but it takes ages to finish: for( i in

Hi, is it possible to merge two data frames while preserving the row names of the bigger data frame? I have two data frames which i would like to combine. While doing so I always loose the row names. When I try to append this, I get the error message, that I have non-unique names. This although I used unique command on the data frame where the double inputs supposedly are thanks for the help

Hi everybody, I would like to know whether it is possible to compare to tables for certain parameters. I have these two tables: gene table name chr start end str accession Length gen1 4 646752 646838 + MI0005806 86 gen12 2L 243035 243141 - MI0005821 106 gen3 2L 159838 159928 + MI0005813 90 gen7 2L

Hello all R users, I have a problems transforming (or maybe better regrouping) a data.frame. I have a big data.frame, which I would like to sum up according to a specific column. This is an example of my matrix: ID gen 0042787 gen2 0016070 gen2 0016070 gen3 0007409 Gen1 0007409 gen3 0006511 gen2 0006417 gen3 0016070 gen4 0006511 gen4 I want to rearrange the matrix

Hello, I was wondering whether there is a possobility to add File types to the list of filters known by R. I'm using the function choose.files in Windows. I have some files I always use and i would like to filter my option to these kind of files. I have some "atr", "cdt", "gct", "gmt" etc. Is there a way of telling R to filter only these files?

dear all, I have a problem with a masked object in a package we created here. we make a package for a workflow of internal analysis of microarray data. to create the package we used: > install.packages(pkgs="affyAnalysis", repos=NULL) > R CMD INSTALL affyAnalysis Erzeuge Verzeichnisse ... Erzeuge DESCRIPTION ... Erzeuge NAMESPACE ... Erzeuge Read-and-delete-me ... Kopiere

Hello everybody, I'm trying to install a package I have built. This package contains three scripts with various functions (S3 as well as S4 classes) I run at first the package.skeleton command with: > package.skeleton("affyAnalysis", namespace=TRUE, code_files =c("defS3.R", "defS4.R", "qc.R")) affyAnalysis is the name of the supposed package and

Hello, I have two tab-delimited files which I would like to combine. In the first one I have gene IDs (Unique) on column 1 and than various experimental results from microarray analysis (see attached files list1 ) the second arrays have the same genes IDs (more and in a different order, some are double) (see attached files list2 ) What I would like to do is to search in the second list for gene

Hello, Since this an R package, I'm sending the email. I'm loading all the jar files as: library(rJava) hadoop <- Sys.getenv("HADOOP") allfiles <- c(list.files(hadoop,pattern="jar$",full.names=T),list.files(paste(hadoop,"lib",sep=.Platform$file.sep,collapse=""),pattern="jar$",full.names=T)) allfiles <-

I am running Red Hat 7.3 and samba 2.2.3a I can see the samba server in network neighborhood however when I try to connect I receive the following error: \\Puddles is not accessible A network error has occurred. You might not have access to some network resources my smb.conf file is as follows: [global] workgroup = POND encrypt passwords = yes security = SHARE [homes] guest OK =

>> I checked my /etc/group for irregular entries and repaired >> all of them. Since then the problem didn't occur any more. >> Even so it wasn't very frequent. >> >> I still have a bunch of strace logs of smbd and of nscd. >> Cann I upload it somewhere for you if you can use it? >> >> Or do you suggest to replant the erroneous entries and