“\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. ______________________________________________ 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.