UPDATE
this is wrong because the file is a csv file. read_excel is designed
for xls files.
GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM
protein_expression.csv")
How did you get a csv? it downloads as tsv.
the statement you should use is in base, no library() statement is needed.
GBM_protein_expression <- read.delim("C:/Users/Spencer/Desktop/GBM
protein_expression.csv")
read.delim is the same as read.csv except that it sets the sep
argument to "\t".
On Wed, Dec 26, 2018 at 11:11 PM Spencer Brackett
<spbrackett20 at saintjosephhs.com> wrote:
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readxl works best with a newer version of the tibble package.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 at 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 at 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 at 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 at 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 at 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 at 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 at 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 at 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*:
*File for LGG protein expression:* *
<
* 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
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