search for: picr

...s, see the openVignette help page. Loading required package: reposTools Welcome to 'simpleaffy' V 2.1.3 Produced by The Paterson Institute for Cancer Research and funded by CANCER RESEARCH UK. http://bioinformatics.picr.man.ac.uk/simpleaffy mailto: microarray at picr.man.ac.uk Background correcting Retrieving data from AffyBatch...done. Computing expression calls... .........................done. scaling to a TGT of 100 ... Scale factor for: 0203_YH10_H_MCF7_r1.CEL 0.2916602893015...

Hi, We're looking for a number of people to join our group (Applied Computational Biology and Bioinformatics -- ACBB) and applying state of the art techniques (see for example, xmap.picr.man.ac.uk) to integrate, analyse and interpret datasets arising from the latest generation of microarrays (including exon, SNP and tiling arrays), quantitative mass-spectrometry and next generation sequencing. We write a lot of Bioconductor and R code - hence my posting to this list... I've i...

...ffymetrix microarray experiments. We are an interdisciplinary team that brings together skills in computer science, biology and mathematics, and are focused on the development and application of bioinformatics tools to support the interpretation of complex datasets (see, for example, http://xmap.picr.man.ac.uk <http://xmap.picr.man.ac.uk/> ). The ideal candidate will be excited by the interface between computer science, mathematics and biology, and will have a strong desire to see their work applied directly in collaboration with both bench-scientists and clinicians. Significant programmi...

...me. > My guess is that > the problem is using a filename that starts with ".". I see > many packages > put the .First.lib in zzz.R, so I just follow that. > > HTH, > Andy > > > -----Original Message----- > > From: Crispin Miller [mailto:CMiller at PICR.man.ac.uk] > > Sent: Tuesday, October 07, 2003 10:00 AM > > To: R-help (E-mail) > > Subject: [R] .First.lib doesn't appear to be running after > > calling library() > > > > > > Hi - so I've dusted off the C bits of my brain and gotten a > &g...

...ffymetrix microarray experiments. We are an interdisciplinary team that brings together skills in computer science, biology and mathematics, and are focused on the development and application of bioinformatics tools to support the interpretation of complex datasets (see, for example, http://xmap.picr.man.ac.uk ). The ideal candidate will be excited by the interface between computer science, mathematics and biology, and will have a strong desire to see their work applied directly in collaboration with both bench-scientists and clinicians. Significant programming experience is a pre-requisite and...

Hi, I've got a quick question about file permissions and packages... I'm creating my own package, and am having problems with its vignette not being seen when I install it into R... As I understand it, the permissions of the source tree should be as follows: o Directories - drwxrwxr-- o Files - -rw-r--r-- Everything builds and runs through 'R CMD check' fine with

Hi, Forgive a very basic question... I need to take two lists-of-lists, and apply a function to each pair of elements in the lists to return a single list... For example l1 <- list(1:5,6:10,2:15) l2 <- list(1:8,4:12,1:19,4:20) I could easily do an lapply across each of them, but is there a function that does a sort-of pairwise-apply across both together? Does anybody know of a good

My machine has 8GB memory. I had quit all other programs that might take a lot of memory when I try the script (before I post the first message in this thread). The cdf file is of only 741 MB. It is strange to me to see the error. On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber <whuber at embl.de> wrote: > Dear Peng Yu > > how big is the RAM of your computer? You could try with

Hi, Does anyone have any advice on speeding up R functions (short of re-implementing them in C :-) )? I have a function that applies a wilcoxon test to 12 sets of about a quarter of a million pairs (and takes about 3 hours). I've replaced the inner loop I had originally with a function call via mapply, and also considered different approximations of the wilcoxon, rather than that which is

Hi - so I've dusted off the C bits of my brain and gotten a library written for my package... It passes R CMD check ok, and I've put a file called '.First.lib.R' in the pacakge's 'R' subdirectory. Its permissions are 644. It says: .First.lib <- function(lib,pkg) { library.dynam("foo",pkg,lib); require(affy,quietly=TRUE); } I build and INSTALL

Hi, I have a string representing an environment: "bob" And an environment > bob <environment: 0x3901234ac> How do write a function that takes the string and returns the environment? Crispin -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Hi, Does anyone know whether it is possible to construct a colour for plotting with an alpha value as well as simply specifying rgb values? Crispin -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Hi, I have a piece of code that decides at runtime whether to load a data package (and which package to load). This is then done with a call to: library(x) (where x is a character variable containing the package name). This causes R CMD check to throw out a warning: 'library' or 'required' calls not declared from: x Does anyone have any suggestions as to a fix or

Dear all, Im' using matrix() and layout() to set up a fairly complex plot... I was wondering if anyone can point me to something that describes the appropriate incantations to determine, given a text string, the maximum font size that will allow it to fit into the current plotting area without being trunucated? best wishes, Crispin --------------------------------------------------------

Hi, I use RMySQL to connect to MySQL server where I have a couple of stored procedures. I know that the function for the stored procedures "is not yet implemented", but I was trying to get around the problem connecting like that: drv <- dbDriver("MySQL") con <- dbConnect(drv,user=MyUser, password=MyPasswd, dbname=MyDBName, host=MyHost, client.flag="196608"

I was trying to email directly the developer, David A. James, but all the emails bounce... Does anyone know if RMySQL may be re-compiled under Windows and what are the limitations? Cheers, Michal -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}

Hi, I've got a quick question about what happens when indexing into matrices with a single column. I was wondering if anyone can help ... For example: > x <- matrix(1:10) > y <- cbind(x,x) > x[4:6,] [1] 4 5 6 > y[4:6,] [,1] [,2] [1,] 4 4 [2,] 5 5 [3,] 6 6 > class(x[4:6,]) [1] "integer" > class(y[4:6,]) [1] "matrix" It seems that R

Hi, I decided to upgrade to 1.8 today... :-) Anyway, we are writing our own package that is dependent on a bioconductor library - 'affy'. I've checked and when I fire up R, library(affy) behaves as expected... so it all seems to be installed and OK... In the DESCRIPTION file in my package source I have the line: Depends: affy When I run R CMD check simpleaffy I get to: ... *

>> I have a function that applies a wilcoxon test to 12 sets of about a quarter of a million pairs > ... and let me guess: everything is significiant to an almost arbitrary > value of \alpha? :-) For each of quarter of a million sets, I do a wilcoxon between two pairs each containing twenty numbers... I do this 12 times... > > (and takes about 3 hours). I've replaced the