similar to: Possible bug in accessing methods documentation?

On 10/11/2006 2:48 PM, Seth Falcon wrote: > Hi, > > Reading help("Documentation"), I'm led to believe that a help call > like: > > ?myFun(x, sqrt(wt)) > > Will search for help on the appropriate method in the case that myFun > is generic. This isn't working for me. Here is an example using the > Biobase package: > > ## If Biobase is

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, Is there a way to define a custom unary operator in R (other than making a class and 'overloading' the normal unary operators in R)? The documentation seems to suggest that only custom binary operators are possible with the ``%abc%``construct but I was wondering whether any one has done so. None of the RSiteSearch or RSeek queries I posed suggested that this question had

Running R2.4.0 on Apple Mac OS X 10.4.8, in Emacs ESS mode, and also R.app. In an attempt to learn a bit more about a particular method (geneNames in package affy) I invoked getMethods("geneNames") which produced geneNames methods, but not the one in affy (output below). I had to know the signature (AffyBatch) in order to find the method > getMethod("geneNames",

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 All, I need your help. I am analysing affymetrix data and have to select the probe-set that has median expression among all the probe-sets for same gene. This way I want to remove the redundancy by keeping the analysis to single gene entry level. I am fully aware that it is not a nice thing to do but I just have to do it. To do so, I came across 'findLargest' function of

Dear all, i try to plot with ggplot2. Therefor I have an matrix with 3 colums. With cbind I add an additional column called "col". I need this column "col" because in a later step and want to specify here some plot details which I will get from another analysis If I want to plot with this code, I have the problem that the legend is wrong. Blue changed to green and green to

Hello Everyone, I am writing programs in R from 7 months and I am able to solve most of the errors/issues except for this current post. My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains the Microarray Expression Values collected from the Illumina Microarray experiment. These collected intensity values need to be normalized(Rank Invariant Normalization) by using the R

Hi, I want to change .RDA file to a text file. So I did as follows. >load("my.rda") >ls() ---> then it showed [1] exprs >write.table(exprs,"C:\\my.txt",sep="\t") I was successful with the first .RDA file. Then I used the same commands with another .RDA file (172 MB)which is 4 times bigger than the first file (41.2 MB). When I put the last command

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

Hi, I use write.table() to write a file to an external xls file. the column names left-shift one position in output file. I check with col.names() row.names(), the file is fine. How to prevent the shifting? I71 I111 I304 I307 I305 I306 I114 I72 AFFX-BioB-5_at 6.66435 6.787807 5.335962 5.250163 6.47423 5.882104 5.965109 6.591687195 AFFX-BioB-M_at 6.163227 5.965427 4.665569 2.743531 6.097244

I am very new to R. I was trying to load some publicly available Expression data in to R. I used the following commands mydata<-read.table("dataALLAMLtrain.txt", header=TRUE, sep ="\t",row.names=NULL) It reads data without any error Now if I use edit(mydata) It shows only 3916 entries, whereas the actual file contains 7129 entries) My data is something like Gene Description

Hello, I am to run this R script but i keep getting this error. > expr<-exprs(golubMerge) Warning message: The exprSet class is deprecated, use ExpressionSet instead I tried to find information on the website but no luck. (exprSet...etc) thank you. -- View this message in context: http://www.nabble.com/expression-matrix-tp15912874p15912874.html Sent from the R help mailing list archive

Hi, I am relatively new to R and Bioconductor and am trying to filter the topTable that I generated of differentially expressed genes from my normlized eset file comprised of ~ 40 HG-133A Affy microarrays . I would like to see if particular probesets are represented in this list. Alternatively I would like to generate a topTable of differentially expressed genes using only specified probesets

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, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4

Hi, I am having troubles with creating an eSet and would appreciate any help on the following problem. I am trying to create an eSet using the following code pd <- read.table(file="pdata.txt",header =TRUE,row.names=1); colnames(pd) <- c("type","tumor","time","id"); pdN <- list(type =

Hello, I am looking for an explanation and/or fix for a discrepancy in the behaviour of the R lm.influence() function [ version R 1.5.0 (2002-04-29) ] and the same function in Splus [ Splus version 5.1 release 1, running on SGI IRIX 6.2]. The discrepancy is of concern because I am migrating some Splus scripts to R and need to ensure consistency of results. Specifically, when I fit a glm()

Hello all, I have a data file table.txt which i have attached. I am trying to pass the columns as arguments to a function "totnorm" where i am displaying a total normalization plot. The function is given below: totnorm<-function(x,y){scale<-sum(x)/sum(y);xlab<-colnames(x);ylab<-colnames(y);x1<-x[[1]];y1<-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6, col.lab=4);}

Hello all, I have a data file table.txt which i have attached. I am trying to pass the columns as arguments to a function "totnorm" where i am displaying a total normalization plot. The function is given below: totnorm<-function(x,y){scale<-sum(x)/sum(y);xlab<-colnames(x);ylab<-colnames(y);x1<-x[[1]];y1<-scale*y[[1]];plot(x1,y1,xlab=xlab,ylab=ylab,col=6, col.lab=4);}