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...quot;http://bioconductor.org/biocLite.R") BiocInstaller version 1.2.1, ?biocLite for help > biocLite("lumi") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'lumi' Installing package(s) into ‘/home/hnorpois/R/i686-pc- linux-gnu-library/2.14’ (as ‘lib’ is unspecified) Warnung: dependency ‘hdrcde’ is not available versuche URL ' http://www.bioconductor.org/packages/2.9/bioc/src/contrib/lumi_2.6.0.tar.gz' Content type 'application/x-gzip' length 11386679 bytes (10.9 Mb) URL geöffnet =====...

Hello, I wish to count how often zero (0) appears in the vector test. test [1] 1 1 1 1 1 1 2 1 1 1 0 2 0 1 1 0 0 0 1 1 1 0 1 2 1 1 1 1 1 1 I think of something like ... > sapply (test, function (x) if (x==0 ... ... but actually I dont know how to carry on. Could anybody give me a hint? Thanks Hermann [[alternative HTML version deleted]]

Hello, I have a vector (numeric) v-> c(a,b,c,d,e) and I want to create the vector n->c(b-a,c-b,d-c,e-d). How can I do that? Thank you Hermann [[alternative HTML version deleted]]

Hello, I would like to transform a character vector into a "binary" vector ("keine" and " " become 0 and the rest 1). > dput (scm) c("keine", " ", "keine", "Erstgradverw.", "Mutter", "Erstgradverw.", "Erstgradverw.", "keine", " ", "Vater",

Dear list, I wish to plot chromatin precipitation data: I would like to have a rectangles (x:end-start, y:peak) but I do not have an idea how to define x (in terms of qplot syntax) and to choose the correct geom. mydata is a subset of a larger file. > mydata chrom start end peak 1 chr11 5291000 5291926 8 2 chr11 10988025 10988526 7 3 chr11 11767950 11768676 8 4

Hello, my data is sorted by start.ens (see below). And now I would like to extract all rows (so called* defined row*s) with type==Expression - subset (df, type==Expression) - and the aforegoing type==DNase HS (which is not necessarly row n-1 - assumung that the defined row is n). I dont know how to add this to my subset command. Is that possible? Thanks Hermann > df start.ens fc.trans

Hello, I have a list with gene names, fold changes (=expression level) and chromosomes. Names fold change chromosome hz 1.5 2 If I plot fold change versus chromosome (or vice versa): plot (ch, fc) I see only the chromosomes with numbers but not those with letter (x and y). What can I do? A second question: How can I add a single line in that plot at a certain

Hello, having a data frame like test with pairs of characters I would like to create chains. For instance from the pairs A/B and B/I you get the vector A B I. It is like jumping from one pair to the next related pair. So for my example test you should get: A B F G H I C F I K D L M N O P > test V1 V2 1 A B 2 A F 3 A G 4 A H 5 B F 6 B I 7 C F 8 C I 9 C K 10 D L

Hello, I have start and end coordinates from different experiments (DNase hypersensitivity data) and now I would like to combine overlapping intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101 are combined to 30-101. But 49-101 and 70-103 would not be combined because they are on different chromosomes (chr a and chr b). Does anybody have an idea? Thanks Hermann > df

Hello, I open some files in a directory and get a list. open.list <- sapply (namen, function (x) {file <- list.files (ddir, pattern=x, full.names=TRUE) # namen is vector and each element detects a special file to open file <- read.table (file) } ) This list has no names. I would like to get a list with key/value

Dear list, I have a problem with defining a function (see below) to read my testfile (see testfile). My function only returns mydata I wish to work with attr(mydata, 'fc') as well (for labelling a plot). Principally it works if I do not insist on this function but it would be much easer if it is possible to return mydata AND attr(mydata, 'fc') by using a function. 1) testfile:

Hello, I did a pca with over 200000 snps for 340 observations (ids). If I plot the eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot (rotation[,2]) I see a strange "column" in my data (see attachment). I suggest it is an artefact (but of what?). Suggestion: I used prcomp this way: prcomp (mat), where mat is a matrix with the column means already substracted followed by a