search for: ganzfried

...an R package and I was wondering if anyone knows how to include institution name in the "Description File." That is, my current Description File looks like: Package: curatedCancerData Type: Package Title: Cancer Gene Expression Analysis Version: 1.0 Date: 2011-12-24 Author: Benjamin F. Ganzfried, et al. Maintainer: Benjamin F. Ganzfried <ben.ganzfried@gmail.com> Description: The curatedCancerData package provides relevant functions and data for gene expression analysis. License: GPL (>= 3) Ideally I would like the final PDF to have footnotes showing the university affiliations o...

...#39;ve read the regular expression tutorial for R, but could only figure out how to grab an integer value if it is the only integer value in the row (ie more than one integer value makes this basic regular expression unsuccessful). Thank you very much for any help you can provide. Sincerely, Ben Ganzfried [[alternative HTML version deleted]]

Hey, I'm trying to match patient identifiers from two separate input files, and then add information from one of the input files to the corresponding output file. I'd greatly appreciate any help! More specifically, Input_File_1 has a column header "bcr_patient_barcode" Input_File_2 has a column header "Barcode" and a column header "Batch" I want my script

Hi guys, My code (next 2 lines below) isn't doing what I'm expecting it to: tmp <- ifelse(uncurated$days_to_tumor_recurrence=="null","norecurrence","recurrence") curated$recurrence_status <- tmp I want the column "recurrence_status" in my output file to have values "recurrence" (if the input value had a number in the

I'm looking over good-code a post-doc in my lab wrote and trying to learn how it works. I came across the following: rel.abundance <- as.matrix(read.delim("rel.abundance.csv",row.names=1,as.is =TRUE)) rel.abundance <- log2(rel.abundance-min(rel.abundance)+1) I'm not sure what the second line is doing. I ran each line in R and couldn't see a noticeable difference in

Hi-- I'm creating an R package, I've read through "Writing R Extensions" and the package.skeleton() R page-- and I'm still running into a little confusion. I would greatly appreciate any advice you can provide. Where do I run my following line of code from?: > package.skeleton(name = "a", code_files = "EsetObject.r" I'm currently running it from

Hi -- I had a pretty quick R question since unfortunately I have not been able to find an answer on Google. It shouldn't take much more than a minute to answer. I'm trying to add up the major gleason grade and minor gleason grade for an analysis of patients with prostate cancer. One column has values under "Major Gleason" and another column has values under "Minor

Hey, I just googled my error and many things came up. I followed the leads and read the ?read.delim page; I tried changing header = TRUE, and row.names = TRUE-- but I've still been having trouble fixing it, so I would greatly appreciate any help you can provide. Here is my code: rm(list=ls()) source("../../functions.R") uncurated <-

Hi-- I googled the above error and found previous postings about this error on the list. I was having a little difficulty implementing the advice though. The suggestions were to use: traceback() and checkRd(). I'm using R in the directory in which the .Rd file with the problem is located, but I'm having difficulty figuring out how to proceed. I've looked through the help pages for

Hey, I keep getting the following warning: > data(GSE19829-GPL570_eset) Warning in data(GSE19829 - GPL570_eset) : data set ‘GSE19829 - GPL570_eset’ not found > ## maybe str(GSE19829-GPL570_eset) ; plot(GSE19829-GPL570_eset) ... > > if(require(affy)){ + summary(GSE19829-GPL570_eset$vital_status) + } Error in summary(GSE19829 - GPL570_eset$vital_status) : object

Hi, I'm trying to build a Forest Plot using the second and fourth columns in the table (test.csv) below. My code is the following: curated <- data.frame("test.csv") tmp <- curated$coef tmp1 <- curated$se_coef plt <- metaplot(tmp, tmp1, xlim = c(-.45, .45)) I keep getting the following error at the last line and am not sure why: Error in if (is.na(lower[i] + upper[i]))

...his is a bioconductor question so please ask on the > Bioconductor mailing list. Good news, you don't have to subscribe to post > > http://bioconductor.org/help/**mailing-list/<http://bioconductor.org/help/mailing-list/> > > Martin > > > On 10/07/2011 07:27 AM, Ben Ganzfried wrote: > >> 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 >...

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, My project is set up the following way: root directory contains the following folders: folders: "Breast_Cancer" AND "Colorectal_Cancer" AND "Lung_Cancer" AND "Prostate_Cancer" I want to create a file, call it: "repeating_functions.R" and place it in the root directory such that I can call these functions from within the sub-folders in each

Hi-- I'm trying to teach myself R using Peter Dalgaard's "Introductory Statistics with R." Does anyone know if there are solutions available for the exercises? I'm really just hoping to learn by going through exercises and checking myself, so alternatively, does anyone know of an introductory textbook to R that does have answers available either in the back or online?