[R] Fwd: UPDATE

[Spencer Brackett]

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readxl works best with a newer version of the tibble package.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.
>>>
>>

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