On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
<spbracket...@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.calb...@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
______________________________________________
R-help@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.
