CSV and TSV are not Excel files. Yes, I know Excel will open them, but that does not make them Excel files.
Read a TSV file with read.table or read.csv, setting the sep argument to "\t". On December 26, 2018 7:26:35 PM PST, Spencer Brackett <spbracket...@saintjosephhs.com> wrote: >I tried importing the file without preview and recieved the >following.... > >library(readxl) >> GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM >protein_expression.csv") >Error: Can't establish that the input is either xls or xlsx. >> View(GBM_protein_expression) >Error in View : object 'GBM_protein_expression' not found >Error in gzfile(file, mode) : cannot open the connection >In addition: Warning message: >In gzfile(file, mode) : > cannot open compressed file >'C:/Users/Spencer/AppData/Local/Temp/RtmpQNQrMh/input147c61fc5b52.rds', >probable reason 'No such file or directory' >> library(readxl) >> GBM_protein_expression <- >read_excel("C:/Users/Spencer/Desktop/GBM_protein_ expression.xlsx") >readxl works best with a newer version of the tibble package. >You currently have tibble v1.4.2. >Falling back to column name repair from tibble <= v1.4.2. >Message displays once per session. >> View(GBM_protein_expression) > >Also, the area above my console says that no data is available in the >table. Is this perhaps the result of lack of preview or the fact that >the >excel file itself contains no numerical data, but only TRUE or FALSE >entries? > >On Wed, Dec 26, 2018 at 9:57 PM Spencer Brackett < >spbracket...@saintjosephhs.com> wrote: > >> 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 >> >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. -- Sent from my phone. Please excuse my brevity. ______________________________________________ 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.