[R] you are making it far too difficult

[Spencer Brackett]

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 using 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]]