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
Help converting .txt to .csv file
6 messages · Bert Gunter, Richard M. Heiberger, Spencer Brackett +1 more
Inline. -- Bert Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Wed, Dec 26, 2018 at 3:04 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) ... 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,
Huh?? Why do you think this? A csv is just a comma delimited text file. R can input pretty much any kind of file, ONCE YOU KNOW THE FORMAT OF WHAT YOU ARE INPUTTING. This should be provided by the links that you gave. Then see ?read.table or, more generally, ?scan for how to read the (text) file into R into whatever data structure you need. See also the R data import/export manual. Or possibly post to the Bioconductor list where they specialize in this sort of thing and may already have packages that can access the repositories and bring in the data in the form you need them. They also have lots of software there for analysis, too. Cheers, Bert
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 at 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.
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]]
______________________________________________ R-help at 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.
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
[[alternative HTML version deleted]]
______________________________________________ R-help at 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.
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
[[alternative HTML version deleted]]
______________________________________________ R-help at 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.
Hi See inline
-----Original Message----- From: R-help <r-help-bounces at r-project.org> On Behalf Of Spencer Brackett Sent: Thursday, December 27, 2018 3:57 AM To: Richard M. Heiberger <rmh at temple.edu> Cc: R-help <r-help at r-project.org> Subject: Re: [R] Help converting .txt to .csv file 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
You forgot to add read.* function. something like protein_expression <- read.delim(file.choose()) or protein_expression <- read.table(file.choose(), header=TRUE, sep="\t") If your files are tab delimited as Richard suggested. Cheers Petr
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]]
______________________________________________ R-help at 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 at 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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