[R] you are making it far too difficult

Thu Dec 27 22:53:03 CET 2018

Thank you!

On Thu, Dec 27, 2018 at 4:43 PM Sarah Goslee <sarah.goslee using gmail.com> wrote:

> \t is the symbol for a tab.
> /t is two characters just as it seems. It's highly unlikely your file
> is delimited with /t, which would look like
> 1/t2/t3
>
> The help for read.table mentions this tangentially as part of
> read.delim(), and you can find out more under ?regex - see the section
> about escaping non-metacharacters with a backslash.
>
> Sarah
>
> On Thu, Dec 27, 2018 at 4:09 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
>

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