[R] Fwd: UPDATE

[Jeff Newmiller]

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 <spbrackett20 using 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readxl works best with a newer version of the tibble package.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 <
>spbrackett20 using 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 <
>> spbrackett20 using 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
><rmh using 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
>>>> <spbrackett20 using 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 using 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 using 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.