[R] you are making it far too difficult

[Sarah Goslee]

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