[R] Fwd: UPDATE
Spencer Brackett
@pbr@ckett20 @ending from @@intjo@ephh@@com
Thu Dec 27 05:07:32 CET 2018
Sorry, my mistake.
So I could still use read.table and should I try using a .txt version of
the file to avoid the silent changes you described?
Also, when I tried to simply this process by downloading the dataset onto
RStudio opposed to R (Gui) I received 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readxl works best with a newer version of the tibble package.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)
Is this perhaps the result of lack of preview (which I did not complete at
the time I hit import as the preview failed to load), or the fact that the
excel file itself contains no numerical data, but only TRUE or FALSE
entries?
On Wed, Dec 26, 2018 at 10:59 PM Jeff Newmiller <jdnewmil using dcn.davis.ca.us>
wrote:
> Please always reply-all to keep the list involved.
>
> If you used Save As to change the data format to Excel AND the file
> extension to xlsx, then yes, you should be able to read with readxl. I
> don't recommend it, though... Excel often changes data silently and in
> irregularly located places in your file.
>
> On December 26, 2018 7:38:16 PM PST, Spencer Brackett <
> spbrackett20 using saintjosephhs.com> wrote:
> >So even if I imported the file form ICGC to my desktop as an excel
> >file,
> >and can view and saved the data as such, it is still a TSV?
> >
> >On Wed, Dec 26, 2018 at 10:35 PM Jeff Newmiller
> ><jdnewmil using dcn.davis.ca.us>
> >wrote:
> >
> >> 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.
> >>
>
> --
> Sent from my phone. Please excuse my brevity.
>
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