search for: affy

I am getting the following error in my script. I am very very new to R and have obtained this script from another person. #read file in (dummy data) starburst.plot<-function(affy.fold, affy.FDR)(ifelse( ((affy.fold) >=0), -1*log10(affy.FDR), 1*log10(affy.FDR))) starburst.plot<-function(meth.fold, meth.FDR)(ifelse( ((meth.fold) >=0), -1*log10(meth.FDR), 1*log10(affy.FDR))) At my next command, I get the following error: > g.ex.affy <- starburst.plot(data(,&qu...

Hi!I'm doing a little data importing from .cel files, > setwd("/home/mandova/celfiles") > mydata<-ReadAffy() Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried > filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") > filenames<-as.character(filenames) > filename...

Hello, I am trying to install affy package in R as follow: >R CMD INSTALL -l lib ~/rstuffs/affy_1.4.32.tar.gz Then I get an error at the end: Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts,...

...esent chip and rows represent genes. Now, the biplot function biplot(prcomp(pcadata, scale = TRUE), cex = c(0.75,0.75)) gives me a plot with one vector per gene. However, I actually need to get one vector per chip instead of one vector per gene. I have been told that there is a function in the affy package that does what I am looking for i.e. gives one vector per chip. Can someone please tell me what the function is called, and how I can get hold of the code(since I believe affy only works on CEL files) ? I have downloaded the affy R code from Terry Speed's website already, but I don'...

Hello, I have a problem with read.affy.mixed function. I want to read in together a set of CEL files from chip types Affymettrix HGU133A_2 and HGU133_Plus_2. I have my files to be read in in one directory together with a white space delimited file describing them (covdesc). In this directory I give a command: > merge <-...

Hi, I am looking for a way to find out the version information of installed R packages. ex: >library(affy) >SOME_COMMAND_FOR_VERSION(affy) I know I can do either getRversion() or R.Version() could give me the version of R. I assume there must be a way for me to get version information for the add-on paclages,right? Thanks! Yupu

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: ... * checking package dependencies ... ERROR Pack...

Dear All, There is a question I met when using Affy package in Bioconductor. I asked it in BioC and didn't get any responses. Sorry to post again: Could anyone tell me how to draw a deep-blue Affymetrix image through Image() function in Affy package? The default settings of image() draw me a black-white image and if I modify it to 256 colors...

Does anyone have nice quality controlls for affy arrays,.... Can't find any tools as are being used for 2 dye arrays..... cheers, marinus This e-mail and its contents are subject to the DISCLAIMER at http://www.tno.nl/disclaimer/email.html [[alternative HTML version deleted]]

Hello, I am trying to call R from Perl running on Windows 2000. I have looked through the previous posts regarding running R from Perl and all have referred to the RSPerl package at Omegahat. Unfortunately the documentation for this package specifically states that it only works in Unix at the moment. Does anyone else have any suggestions about the best way to do this in the Windows

...' package which I installed in R 2.11.1 on Windows. I thought I'd test out the function first with the examples they give in the documentation: # foo example test <- matrix(c(1,1,4,1,1,6,1,10,3,2,1,5,2,2,6,2,4,8),byrow=TRUE,6) mhtplot(test) mhtplot(test,logscale=F) # fake example with Affy500k data affy <-c(40220, 41400, 33801, 32334, 32056, 31470, 25835, 27457, 22864, 28501, 26273, 24954, 19188, 15721, 14356, 15309, 11281, 14881, 6399, 12400, 7125, 6207) CM <- cumsum(affy) n.markers <- sum(affy) n.chr <- length(affy) test <- data.frame(chr=rep(1:n.chr,affy),...

...tely reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and sessionInfo(). Thanks, Mark > setwd("~/Genomics/Experiments.Genomic/BB01/acb.shell") > local(save(affy.object.preprocessed, file ="affy.object.preprocessed.R" )) > load("affy.object.preprocessed.R") Error in load("affy.object.preprocessed.R") : ReadItem: unknown type 65, perhaps written by later version of R > sessionInfo() R version 2.5.0 Under development (u...

...tely reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and sessionInfo(). Thanks, Mark > setwd("~/Genomics/Experiments.Genomic/BB01/acb.shell") > local(save(affy.object.preprocessed, file ="affy.object.preprocessed.R" )) > load("affy.object.preprocessed.R") Error in load("affy.object.preprocessed.R") : ReadItem: unknown type 65, perhaps written by later version of R > sessionInfo() R version 2.5.0 Under development (u...

Hi, all. Something strange happened to my ESS. I use Mac OS X. When R is used in stand alone mode, it recognizes external libraries like "affy", "e1071" etc. However, when R is invoked through ESS in Emacs, it produces errors like: Error in library(affy) : There is no package called 'affy' Interestingly, I remember I successfully used these libraries through ESS in Emacs before. I became unable to use these librar...

I would like to build a package for the HT HG-U133+ PM arrays from affy, but I can't find any good documentation on how to go about it. Naively using makecdfenv's make.cdf.package() causes R to seg-fault. I'm unfamiliar with the CDF format as such, but I'm guessing that it's changed somewhat because the PM arrays no longer have P/A and mismatche...

Hi! I would like to select probes (affy expression set) of genes that are "cancer-related". Conventionally the decision whether a gene is cancer-related or not is made by looking up the literature. Since this is not possible for all genes on the array I wonder if there is a way of doing this automatically? Best wishes Kri...

...ween one chromosome and the next) but I just want to put the chromosome number in between the two tick markers. This example from mhtplot has the chromosome number at the place of the tickmarker. How can I change this to ???in between???? Thanks!, Naomi # fake example with Affy500k data affy <-c(40220, 41400, 33801, 32334, 32056, 31470, 25835, 27457, 22864, 28501, 26273, 24954, 19188, 15721, 14356, 15309, 11281, 14881, 6399, 12400, 7125, 62 07) CM <- cumsum(affy) n.markers <- sum(affy) n.chr <- length(affy) test <- data.frame(chr=rep(1:n.chr,affy...

...nder Win XP or Linux, but never faced the problem of multiple locations for libraries.) please find below the code form *(a)* launching : Rterm.exe ?vanilla ?q < myRcode.r (where ?local? libs are *NOT found*) :** > .libPaths() "C://PROGRA~1/R/R-26~1.0/library" > require(affy) Le chargement a n?cessit? le package : affy Warning messages: 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : aucun package nomm? 'affy' n'est trouv? > # this translates into "no package called "affy" was found" &...

Hi , I was trying read in an affy array/matrix and then to calculate the mean value for all the duplicates. Is there a function in the R package that would do this? I tried the help function and searched for 'duplicate'. Although it provides a list of functions that would eliminate the duplicate probe ids, I couldn't...

Dear all, I was trying to normalize a subset of affy data those transcribe are either P or M (called pm_filter). I am able to normalize pm_filter subset by using RMA method, however MAS5 is not working. For RMA method, I used the following commend: est<-rma(affydata, subset=pm_filter). Could any help me; how do I do this by using MAS5 method?...