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?) 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 > > -- > Federico Calboli > LBEG - Laboratory of Biodiversity and Evolutionary Genomics > Charles Deberiotstraat 32 > <https://maps.google.com/?q=Charles+Deberiotstraat+32&entry=gmail&source=g> > box 2439 > 3000 Leuven > +32 16 32 87 67 > > > > > >[[alternative HTML version deleted]]
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
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]]