At this point, it seems pretty clear that the issue is in the data file itself. Possibilities are that it is either not a CSV file to begin with or in some exotic encoding (utf-16?).
You probably need to look at the file in a text editor to see whether the context makes sense as comma-separated variables. Also, perhaps review the download mechanism --- recently I have found several students shooting themselves in the foot by downloading .csv files, having them automatically opened by Excel and the save them _in_ Excel, garbling the file in the process. -pd > On 31 Aug 2018, at 03:05 , Spencer Brackett <spbracket...@saintjosephhs.com> > wrote: > > My apologies... the following is what I received from the correction > > the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep=",") > Warning messages: > 1: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 3 appears to contain embedded nulls > 2: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 4 appears to contain embedded nulls > 3: In read.table(file = file, header = header, sep = sep, quote = quote, : > line 5 appears to contain embedded nulls > 4: In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : > embedded nul(s) found in input >> > > > On Thu, Aug 30, 2018 at 8:57 PM Patrick Barry <pdba...@alaska.edu> wrote: > >> You still haven't fixed the first thing both Sarah and I pointed out. You >> are lacking an = between sep and "," >> >> the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") >> >> should be >> >> the_data <- read.csv(file = "GBM_clinical_drug.csv", header = TRUE, *sep >> = ","*) >> >> as Sarah pointed out, you should use spaces to help make these errors more >> obvious. >> >> On Thu, Aug 30, 2018 at 4:53 PM, Spencer Brackett < >> spbracket...@saintjosephhs.com> wrote: >> >>> Hello again, >>> >>> My apologies for the delayed response... computer troubles. In reference >>> to >>> Ms. Goslee's and Mr. Barry's query, the following is the error code >>> received after I inputted my R command >>> >>> the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",") >>> Error: unexpected string constant in >>> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep","" >>> >>> Given this, should I proceed with implementing the path<getwd() ,since I >>> am, as he suggested trying to set the variable *path* to my working >>> directory with path<-"." >>> >>> Mr. Mittal also recommended importing with r studio, which I shall try in >>> the meantime. >>> >>> Many thanks, >>> >>> Spencer Brackett >>> >>> >>> On Wed, Aug 29, 2018 at 10:14 PM Amit Mittal <prof.amit.mit...@gmail.com> >>> wrote: >>> >>>> Use r studio and import from the menu. Read_csv has changed >>>> >>>> Also you can see any format problems >>>> >>>> On Thu, 30 Aug 2018 3:36 am Spencer Brackett, < >>>> spbracket...@saintjosephhs.com> wrote: >>>> >>>>> Good evening R users, >>>>> >>>>> I am attempting to carry out DNA methylation analysis on two separate >>>>> CSV >>>>> files (LGG and GBM), which I have downloaded onto my R console. To set >>> the >>>>> path<-"." to be indicative of one or both of the csv files, I utilized >>> the >>>>> following functions and received the errors shown. How do I set the >>> "." so >>>>> that I can begin analysis on my files? >>>>> >>>>>> the_data <-read.csv(file="LGG_clinical_drug.csv",header=T,sep",") >>>>> Error: unexpected string constant in "the_data >>>>> <-read.csv(file="LGG_clinical_drug.csv",header=T,sep","" >>>>>> the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",") >>>>> Error: unexpected string constant in >>>>> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep","" >>>>> >>>>> This is the preliminary portion of the analysis I am trying to run, >>> which >>>>> I >>>>> am referring to: >>>>> >>>>> 1 library(TCGAbiolinks) >>>>> 2 >>>>> 3 # Download the DNA methylation data: HumanMethylation450 LGG and GBM. >>>>> 4 path <– "." >>>>> 5 >>>>> 6 query.met <– TCGAquery(tumor = c("LGG","GBM"),"HumanMethylation450", >>>>> level = 3) >>>>> 7 TCGAdownload(query.met, path = path ) >>>>> 8 met <– TCGAprepare(query = query.met,dir = path, >>>>> 9 add.subtype = TRUE, add.clinical = TRUE, >>>>> 10 summarizedExperiment = TRUE, >>>>> 11 save = TRUE, filename = "lgg_gbm_met.rda") >>>>> 12 >>>>> 13 # Download the expression data: IlluminaHiSeq_RNASeqV2 LGG and GBM. >>>>> 14 query.exp <– TCGAquery(tumor = c("lgg","gbm"), platform = >>>>> "IlluminaHiSeq_ >>>>> RNASeqV2",level = 3) >>>>> 15 >>>>> 16 TCGAdownload(query.exp,path = path, type = "rsem.genes.normalized_ >>>>> results") >>>>> 17 >>>>> 18 exp <– TCGAprepare(query = query.exp, dir = path, >>>>> 19 summarizedExperiment = TRUE, >>>>> 20 add.subtype = TRUE, add.clinical = TRUE, >>>>> 21 type = "rsem.genes.normalized_results", >>>>> 22 save = T,filename = "lgg_gbm_exp.rda") >>>>> >>>>> Many thanks, >>>>> >>>>> Spencer Brackett >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> ______________________________________________ >>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>>> PLEASE do read the posting guide >>>>> http://www.R-project.org/posting-guide.html >>>>> and provide commented, minimal, self-contained, reproducible code. >>>>> >>>> >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd....@cbs.dk Priv: pda...@gmail.com ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.