similar to: adding column of ordered numbers to matrix

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(";", "\\\",\"",

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

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, 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

Hi all, I want to extract every 20th row of a big matrix, say 10000 by 1000. What is the simper way to do this? Thank you very much! Hannah [[alternative HTML version deleted]]

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

Hi BioC user, I have a problem extracting the gene set I would like to work with. Here is I work with my data: normData <- read.delim("normalizedData.txt",sep ="\t") ######### two class unpaired comparison # y must take values 1,2 classes <- c(-1,-2,1,2) #prepere the data for the samr analysis data.x <-as.matrix(normData[,8:11]) d=list(x=data.x,y=classes,

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",

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, 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?

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

it did help to create the separate vectors. The problem is, I would like to continue working with each vector on its own and make some further analysis. For that i need to allocate each vector in the filePatterns a unique name, which I just can't do. I'm not so great in R loops and the help over the net regards for loops in R is quite rare. I'm really thankful for every help.

Hi, In the order() help file, there is an example like: a <- c(4, 3, 2, NA, 1) b <- c(4, NA, 2, 7, 1) z <- cbind(a, b) (o <- order(a, b)); z[o, ] How can I do something like "order a in ascending order, b in descending order"? And say I have a third vector c, and I'd like to add this to the previous condition "a ascending, b descending, c

Hi, I have a problem on my mac when trying in R to produce png images. I am getting this warnings with the ArrayQualityMetrics package: > arrayQualityMetrics(rma_fatBody, outdir="normData", force =T) The report will be written into directory 'normData'. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 (loaded the KernSmooth namespace) libpng warning: Application built

Dear friends, I want to sort a dataset according to one or two variables in the dataset, i thought sort could do it , but failed. e.g. x <- c(2, 9, 18, 3, 2) y<-c(2,5.6,5,9,8) z<-c(21,5,5,19,7) a<-cbind(x,y,z) a x y z [1,] 2 2.0 21 [2,] 9 5.6 5 [3,] 18 5.0 5 [4,] 3 9.0 19 [5,] 2 8.0 7 I want to sort dataset a according to ascending x and descending y, How to

Dear All, here a problem I think many of you can solve in few minutes. I have a dataframe which contains values of plot id, diameters, heigths and basal area of trees, thus columns names are: id | dbh | h | g head(ipso, n=10) id dbh h g 1 FPE0164 36 13.62 0.10178760 2 FPE0164 31 12.70 0.07547676 21 FPE1127 57 18.85 0.25517586 13 FPE1127 39 15.54 0.11945906 12 FPE1127