Hi See inline
> -----Original Message----- > From: R-help <r-help-boun...@r-project.org> On Behalf Of Spencer Brackett > Sent: Thursday, December 27, 2018 3:57 AM > To: Richard M. Heiberger <r...@temple.edu> > Cc: R-help <r-help@r-project.org> > Subject: Re: [R] Help converting .txt to .csv file > > Hello again, > > I worked on directly downloading the file into R as was suggested, but have > thus far been unsuccessful. This is what I generated on my second attempt... > > GBM protein_expression<-(file.choose(), header=TRUE, sep="\t") > Error: unexpected symbol in "GBM protein_expression" > > GBM You forgot to add read.* function. something like protein_expression <- read.delim(file.choose()) or protein_expression <- read.table(file.choose(), header=TRUE, sep="\t") If your files are tab delimited as Richard suggested. Cheers Petr > protein_expression<-(file.choose(GBM_protein_expression.xlsx),header=TRUE, > sep="\t") > Error: unexpected symbol in "GBM protein_expression" > > > > What part of the argument is in error? > > Also I tried importing the dataset as an excel file on RStudio to see if I > could > solve my problem that way. However, my imported excel file has been stuck in > the 'retrieving preview data' and no data is appearing. Is the data file > prehaps > too large or in the wrong format? > > > > On Wed, Dec 26, 2018 at 6:42 PM Spencer Brackett < > spbracket...@saintjosephhs.com> wrote: > > > Mr. Heiberger, > > > > Thank you for the insight! I will try out suggestion. > > > > Best, > > > > Spencer Brackett > > > > On Wed, Dec 26, 2018 at 6:34 PM Richard M. Heiberger <r...@temple.edu> > > wrote: > > > >> I looked at the first file. It gives an option to download as TSV > >> (tab separated values). > >> That is the same as CSV except with tabs instead of commas. > >> You do not need any external software to read it. Read the > >> downloaded file directly into R. > >> > >> read.delim looks as if it would work directly on the downloaded file. > >> ?read.delim > >> The notation "\t" means the tab character. > >> > >> As an aside, stay away from notepad. it is too naive for almost > >> anything interesting. > >> The specific case I often see is people reading linux-style text > >> files with notepad, which doesn't understand NL terminated lines. > >> nicely formatted text files become illegible. > >> > >> On Wed, Dec 26, 2018 at 6:04 PM Spencer Brackett > >> <spbracket...@saintjosephhs.com> wrote: > >> > > >> > Good evening, > >> > > >> > I am attempting to anaylze the protein expression data contained > >> > within these two ICGC, TCGA datasets (one for GBM and the other for > >> > LGG) > >> > > >> > *File for GBM protein expression*: > >> > > >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22 > >> :%7B%22is%22:%5B%22GBM- > US%22%5D%7D,%22availableDataTypes%22:%7B%22is% > >> 22:%5B%22pexp%22%5D%7D%7D%7D > >> > > >> > *File for LGG protein expression:* > >> > > >> > > >> > * > >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22 > >> :%7B%22is%22:%5B%22LGG- > US%22%5D%7D,%22availableDataTypes%22:%7B%22is% > >> 22:%5B%22pexp%22%5D%7D%7D%7D > >> > < > >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22 > >> :%7B%22is%22:%5B%22LGG- > US%22%5D%7D,%22availableDataTypes%22:%7B%22is% > >> 22:%5B%22pexp%22%5D%7D%7D%7D > >> >* > >> > > >> > When I tried to transfer the files from .txt (via Notepad) to > >> > .csv > >> (via > >> > Excel), the data appeared in the columns as unorganized and random > >> > script... not like how a typical csv should be arranged at all. I > >> > need > >> the > >> > dataset to be converted into .csv in order to analyze it in R, > >> > which is > >> why > >> > I am hoping someone here might help me in doing that. If not, is > >> > there perhaps some other way that I could analyze the datatsets on > >> > R, which > >> again > >> > is downloaded from the dataportal ICGC? > >> > > >> > Best, > >> > > >> > 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. 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