similar to: "text"-function: adding text in an x,y-plot

Hi, The following command: axis(1, at= 1:50, labels= sampleNames(data)) produces an X-axis with 50 ticks and labels drawn from the sampleNames namespace. Problem is the labels at each tick are printed parallel to the x-axis and thus run into each other. How do I specify for the labels to be printed perpendicular to the x-axis? Thanks in advance. Anjan -- =================================== anjan

Hi, I'm very confused about R structures and the methods to go with them. I'm using R for microarray analysis with Bioconductors. Suppose without reading the documentations, what's the best way to explore a data structure when you know nothing about it? I am currently using is() / class() to see what the object is. str() / attributes() to probe inside the object, and

Hey, I have code that can check the quality of a data set we're working with (expression data), and I'm having some trouble writing code that would make the expression data we have tie to other data we want to link it to (called phenotype data). Does anyone have any advice on how I could make a single object that would do this? Other relevant info: I want to use the pdata() function,

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the

Hi all, When I ran a script containing the following codes: png(paste(savepath,"a_rnaplot.png",sep = ""),width = fwidth, height = fheight,pointsize = fpointsize); data_deg <- AffyRNAdeg(data_cel) plotAffyRNAdeg(data_deg,col=cols,lty=1,lwd = "2") #a <- par("fin") legend("bottomright",sampleNames(data_cel),col=cols,lty=1)

after this setClass("A") setGeneric("bar", function(x, y) standardGeneric("bar")) setMethod(bar, signature(x="A", y="A"), function(x, y) {}) setMethod(bar, signature(x="A", y="ANY"), function(x, y) {}) the method for signature c("A", "A") contains package information > str(getMethod(bar,

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in

Hello, After running R CMD check on my package I received the following error on package dependencies: * using log directory 'C:/z-zBackup/Nuvera Bio on Iatros01/Development/RPackages/nvNormalize/nvNormalize.Rcheck' * using R version 2.9.1 (2009-06-26) * using session charset: ISO8859-1 * checking for file 'nvNormalize/DESCRIPTION' ... OK * checking extension type ... Package *

Hi together, we received a question about the bioconductor package, maybe anybody could help the guy and I will deliver the message over our forum to him. If this way is allowed ... Regards Knut Here the question: Hello, I have installed R on a linux machine. I have then installed the biocLite.R package from bioconductor. I wanted to install a few other packages - hgu133plus2cdf, rma . I

Dear R-helpers & bioconductor Sorry for cross-posting, this concerns R-programming stuff applied on Bioconductor context. Also sorry for this long message, I try to be complete in my request. I am trying to write a subset method for a specific class (ExpressionSet from Bioconductor) allowing selection more flexible than "[" method . The schema I am thinking for is the following:

Hello List. I have many files of ECG, each one with 7 column and I need only the second column and the name of each ECG. I am doing this but althought I have various days trying this i haven't gotten, so I ask help with this, if somebody cans help me I'll be so thankfully. --------------------------------------------------------------------------------------------------------

I have been trying to learn the various "apply" functions but am still learning their appropriate use. I appreciate any help the R community can offer me. Sorry for the length of this post. Background: I have data on my hard drive organized in the following manner: The data pertains to many different "samples" of data. (e.g. sample 001, sample, 002, sample 003, etc.) Each

Hi, This is a question of a newbie getting into the exciting world of R. I have several dataframes in the same format as NAD: > NAD[1:3,1:3] Sample.Id Main.abs..1 Main.abs..2 148 10a 0.04836 0.04994 167 11a_1109 0.32245 0.36541 173 11b_1109 0.29293 0.32815 What I want to do is to replace the Sample.Id with a corresponding number.The number

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD

Thanks, Martin. Based on my previous post, I thought of a more general formulation of my question that I think would be helpful to ask here. What's the best way to build an R object that links multiple datapoints about different people? I mean, I happen to have datasets that have individual gene expression data tied to individual patient characteristics (how long they survived, age, gender,

hey, i am using the flickr wrapper for ruby and need to access the tags of a specific photo. i got all the rest working. i must admit i am kind of new to ruby, but i tried and tried and couldn''t figure it out. among other things i want to read geotags like in my example here: http://www.flickr.com/photos/whoisstan/146634506/ i''m sure it is deadsimple and i just overlooked it.