[R] you are making it far too difficult
Spencer Brackett
@pbr@ckett20 @ending from @@intjo@ephh@@com
Thu Dec 27 22:34:25 CET 2018
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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