UPDATE

GBM_protein_expression <- read_excel("C:/Users/Spencer/Desktop/GBM

View(GBM_protein_expression)

library(readxl)
GBM_protein_expression <-

View(GBM_protein_expression)

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readxl works best with a newer version of the tibble package.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

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]]

see

code.

      [[alternative HTML version deleted]]

--
Sent from my phone. Please excuse my brevity.

--
Sent from my phone. Please excuse my brevity.