similar to: Error in read.table(file = file, header = header, sep = sep, quote = quote, : more columns than column names

Hi, First of all, I would like to introduce myself as I will probably have many questions over the next few weeks and want to thank you guys in advance for your help. I'm a cancer researcher and I need to learn R to complete a few projects. I have an introductory background in Python. My questions at the moment are based on the following sample input file: *Sample_Input_File*

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

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 have three columns in an input file: MONTH QUARTER YEAR 2012-07 2012-3 2012 2001-07 2001-3 2001 2002-01 2002-1 2002 I want to make output like so: MONTH QUARTER YEAR 07 3 2012 07 3 2001 01 1 2002 I was having some trouble getting the regular expression to work. I think it should

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, 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]))

Hi, I'm just finishing up 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

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

Your example used one distinct studyno in DF1 and one distinct pf_mcl in DF2. I think that makes it hard to see what is going on, but maybe I completely misunderstand the problem. In any case, let's redefine myDF1 and myDF2. Note that myDF1 contains a studyno not in myDF2 and vice versa. myDF1 <- structure(list(studyno = c("J1000/9", "J895/7", "J931/6",

Dear @William<mailto:wdunlap at tibco.com>, thanks for the feedback. I have tested it on the larger dataset and noticed that it created two variables, pf_raw and pf_curated. The output we were looking for, was one that takes the variable pf_mcl in curated dataset and replaces pf_mcl in matching rows within the raw dataset. @Eric<mailto:ericjberger at gmail.com>?s solution was able to

Dear @Bert Gunter<mailto:bgunter.4567 at gmail.com>, I tried merge and I faced many challenges. @Rui Barradas<mailto:ruipbarradas at sapo.pt> solution is working. From: Bert Gunter <bgunter.4567 at gmail.com> Date: Friday, 13 October 2017 at 22:44 To: Kevin Wamae <KWamae at kemri-wellcome.org> Cc: R-help <R-help at r-project.org> Subject: Re: [R] Populate one data

The most relevant of these is r222856 which reverted a set of broken optimizations in r210006. I'd be happy with just including r222856. Optionally, we could take r222868 and r222871 which correctly restore the optimization. On Mon, Dec 29, 2014 at 2:39 PM, Chandler Carruth <chandlerc at google.com> wrote: > Hey Tom, > > David has pointed out to me that we have some *really*

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 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 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,

I'm trying to populate the column ?pf_mcl? in myDF1 with values from myDF2, where rows match based on column "studyno" but the solutions I have found so far don't seem to be giving me the desired output. Below is a snapshot of the data.frames. myDF1 <- structure(list(studyno = c("J1000/9", "J1000/9", "J1000/9", "J1000/9",

Hi again, I wanted to check in and see if you got my note about the broken link on your site. Thanks! Karen On Monday, October 7, 2019 at 5:05 PM, Karen Woodman <karen at getmailbird.co> wrote: > Hi there, > > I noticed that you have a broken link to a website called Qmail.org. That > site was first published 23 years ago (back in 1996!) but unfortunately, it > is no

Hi there, I got a problem when trying to read in a .cel file using ReadAffy(). R codes: require(affy) ReadAffy(filenames="CH1.CEL") It failed and I got the error, Error in read.celfile.header(as.character(filenames[[1]])) : Is CH1.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats Also, I tried