[R] you are making it far too difficult

Caitlin Gibbons bioprogr@mmer @ending from gm@il@com
Thu Dec 27 22:58:39 CET 2018


I would :)


Sent from my iPhone

> On Dec 27, 2018, at 2:34 PM, Spencer Brackett <spbrackett20 using saintjosephhs.com> wrote:
> 
> So I should use “\t” proceeding on? 
> 
>> On Thu, Dec 27, 2018 at 4:30 PM Caitlin Gibbons <bioprogrammer using gmail.com> wrote:
>> “\t” is an escape sequence which signifies one tab character. “/t” is NOT an escape sequence, and to R, looks like a very brief file path. 
>> 
>> Sent from my iPhone
>> 
>> > On Dec 27, 2018, at 2:09 PM, Spencer Brackett <spbrackett20 using saintjosephhs.com> wrote:
>> > 
>> > What is the significance of using / or \ ?
>> > 
>> >> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.goslee using gmail.com> wrote:
>> >> 
>> >> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
>> >> <spbrackett20 using saintjosephhs.com> wrote:
>> >>> 
>> >>> Thank you for the help! I tried using the read.table command in my
>> >> RStudio
>> >>> using the following argument, and managed to open the file.
>> >>> 
>> >>> GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)
>> >> 
>> >> Note that sep="/t" is NOT the same thing as the sep="\t" you were
>> >> advised to use.
>> >> 
>> >> 
>> >> 
>> >> 
>> >>> 
>> >>> However, my data did not unpack as yours did. I again only received a
>> >> table
>> >>> of true and flase distinctions per column, and my environment tab says
>> >> that
>> >>> there is 0 observations upon 0 variables.
>> >>> 
>> >>> I believe I should be getting data similar to what you got, as it would
>> >>> appear that your’s actually contains relevant gene/protein expression
>> >> info.
>> >>> 
>> >>> On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
>> >>> federico.calboli using kuleuven.be> wrote:
>> >>> 
>> >>>> Once you have your TSV files just use something as
>> >>>> 
>> >>>> x = read.table('protein_expression.tsv', h = T, sep = '\t')
>> >>>> 
>> >>>> Do not copy paste the code of this email because it is formatted and
>> >> would
>> >>>> not work in R.
>> >>>> 
>> >>>> 
>> >>>> Best
>> >>>> 
>> >>>> F
>> >>>> 
>> >>>> PS the data looks like this to me
>> >>>> 
>> >>>> head(x)
>> >>>>  icgc_donor_id project_code icgc_specimen_id icgc_sample_id
>> >>>> submitted_sample_id analysis_id        antibody_id gene_name
>> >>>> 1       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
>> >>>> 2       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
>> >>>> 3       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
>> >>>> 4       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
>> >>>> 5       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
>> >>>> 6       DO12370       GBM-US          SP26475       SA131594
>> >>>> TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
>> >>>>  gene_stable_id gene_build_version normalized_expression_level
>> >>>> verification_status verification_platform
>> >>>> 1             NA                 NA                  -1.1636330
>> >>>> not tested                    NA
>> >>>> 2             NA                 NA                  -1.7969721
>> >>>> not tested                    NA
>> >>>> 3             NA                 NA                  -0.7256390
>> >>>> not tested                    NA
>> >>>> 4             NA                 NA                   0.6498421
>> >>>> not tested                    NA
>> >>>> 5             NA                 NA                  -1.0262844
>> >>>> not tested                    NA
>> >>>> 6             NA                 NA                   1.5186400
>> >>>> not tested                    NA
>> >>>>                                        platform
>> >>>> 1 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 2 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 3 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 4 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 5 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 6 M.D. Anderson Reverse Phase Protein Array Core
>> >>>> 
>> >>>> 
>> >>>> 
>> >>>> experimental_protocol
>> >>>> 1 MDA_RPPA_Core
>> >>>> 
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 2 MDA_RPPA_Core
>> >>>> 
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 3 MDA_RPPA_Core
>> >>>> 
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 4 MDA_RPPA_Core
>> >>>> 
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 5 MDA_RPPA_Core
>> >>>> 
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>> 6 MDA_RPPA_Core
>> >>>> 
>> >> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> >>>>  raw_data_repository          raw_data_accession
>> >>>> 1                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 2                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 3                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 4                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 5                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 6                TCGA TCGA-19-5960-01A-13-1900-20
>> >>>> 
>> >> 
>> >> 
>> >> --
>> >> Sarah Goslee (she/her)
>> >> http://www.numberwright.com
>> >> 
>> > 
>> >    [[alternative HTML version deleted]]
>> > 
>> > ______________________________________________
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>> > 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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