I would :)
Sent from my iPhone > On Dec 27, 2018, at 2:34 PM, Spencer Brackett > <spbracket...@saintjosephhs.com> wrote: > > So I should use “\t” proceeding on? > >> On Thu, Dec 27, 2018 at 4:30 PM Caitlin Gibbons <bioprogram...@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 >> > <spbracket...@saintjosephhs.com> wrote: >> > >> > What is the significance of using / or \ ? >> > >> >> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.gos...@gmail.com> >> >> wrote: >> >> >> >> 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 >> >> >> > >> > [[alternative HTML version deleted]] >> > >> > ______________________________________________ >> > 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. [[alternative HTML version deleted]] ______________________________________________ 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.