What is the significance of using / or \ ? On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.goslee at gmail.com> wrote:> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett > <spbrackett20 at 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 at 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]]
?\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 at saintjosephhs.com> wrote: > > What is the significance of using / or \ ? > >> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.goslee at gmail.com> wrote: >> >> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett >> <spbrackett20 at 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 at 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 at 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.
So I should use ?\t? proceeding on? On Thu, Dec 27, 2018 at 4:30 PM Caitlin Gibbons <bioprogrammer at 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 at saintjosephhs.com> wrote: > > > > What is the significance of using / or \ ? > > > >> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.goslee at gmail.com> > wrote: > >> > >> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett > >> <spbrackett20 at 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 at 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 at 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]]
\t is the symbol for a tab. /t is two characters just as it seems. It's highly unlikely your file is delimited with /t, which would look like 1/t2/t3 The help for read.table mentions this tangentially as part of read.delim(), and you can find out more under ?regex - see the section about escaping non-metacharacters with a backslash. Sarah On Thu, Dec 27, 2018 at 4:09 PM Spencer Brackett <spbrackett20 at saintjosephhs.com> wrote:> > What is the significance of using / or \ ? > > On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.goslee at gmail.com> wrote: >> >> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett >> <spbrackett20 at 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 at 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
Thank you! On Thu, Dec 27, 2018 at 4:43 PM Sarah Goslee <sarah.goslee at gmail.com> wrote:> \t is the symbol for a tab. > /t is two characters just as it seems. It's highly unlikely your file > is delimited with /t, which would look like > 1/t2/t3 > > The help for read.table mentions this tangentially as part of > read.delim(), and you can find out more under ?regex - see the section > about escaping non-metacharacters with a backslash. > > Sarah > > On Thu, Dec 27, 2018 at 4:09 PM Spencer Brackett > <spbrackett20 at saintjosephhs.com> wrote: > > > > What is the significance of using / or \ ? > > > > On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.goslee at gmail.com> > wrote: > >> > >> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett > >> <spbrackett20 at 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 at 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]]