For future reference, I unpacked the full gene expression file from ICGC by directly downloading the following link protein_expression.GBM-US.tsv.gz, and then using the argument Mr. Heiberger layed out.
Best, Spencer Brackett On Thu, Dec 27, 2018 at 4:30 PM Spencer Brackett < spbracket...@saintjosephhs.com> wrote: > Mr. Heiberger, > > I followed your argument and it works. I received the same data. And > yes, ICGC breakes their datasets into separate files based on data type. > Thank you for the pointer on selecting all 50 rows, as I assumed that the > entirety of gene expression data within the data set would be downloaded > through the process you followed, as it does when directly downloading the > file via a tsv.gz download. > > On Thu, Dec 27, 2018 at 4:05 PM Richard M. Heiberger <r...@temple.edu> > wrote: > >> I downloaded the Donors dataset >> >> >> https://dcc.icgc.org/search?filters=%7B%22donor%22:%7B%22projectId%22:%7B%22is%22:%5B%22GBM-US%22%5D%7D,%22availableDataTypes%22:%7B%22is%22:%5B%22pexp%22%5D%7D%7D%7D >> >> by clicking "Export table as TSV". >> >> Then I read it with >> >> donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv") >> >> Here is the transcript. >> >> > donors <- read.delim("~/Downloads/donors_2018_12_27_03_52_03.tsv") >> > donors >> Donor.ID Project.Code Primary.Site Gender Age.at.Diagnosis >> 1 DO10892 GBM-US Brain Female 45 >> 2 DO12328 GBM-US Brain Male 56 >> 3 DO11657 GBM-US Brain Female 73 >> 4 DO13510 GBM-US Brain Female 63 >> 5 DO12670 GBM-US Brain Female 63 >> 6 DO11501 GBM-US Brain Female 59 >> 7 DO13809 GBM-US Brain Female 74 >> 8 DO13647 GBM-US Brain Male 56 >> 9 DO11645 GBM-US Brain Male 73 >> 10 DO14145 GBM-US Brain Female 85 >> Tumor.Stage.at.Diagnosis Survival.Time..days. SSM CNSM STSM SGV >> METH.A >> 1 NA NA True True False False >> True >> 2 NA 154 True True False False >> True >> 3 NA NA True True False False >> True >> 4 NA 1448 True True False False >> True >> 5 NA 772 True True False False >> True >> 6 NA NA True True False False >> True >> 7 NA 213 True True False False >> True >> 8 NA 383 True True False False >> True >> 9 NA 113 True True False False >> True >> 10 NA 94 True True False False >> True >> METH.S EXP.A EXP.S PEXP miRNA.S JCN Mutations Mutated.Genes >> 1 False True True True False False 269 392 >> 2 False True False True False False 192 263 >> 3 False True False True False False 128 209 >> 4 False True True True False False 130 199 >> 5 False True True True False False 142 194 >> 6 False True True True False False 129 190 >> 7 False True False True False False 130 178 >> 8 False True False True False False 116 175 >> 9 False True False True False False 125 174 >> 10 False True True True False False 108 169 >> > >> >> I don't know how to get the download of the whole file. It looks like >> you could page through it with the page menu at the bottom of the webpage. >> If you do that, set it for 50 at a time instead of the default 10. >> >> For the Genes and the two types of Mutation files, it will be more >> nuisance this way because there are about 10000 rows for each of those >> three files, thus about 200 of these statements per dataset. >> >> I think it is time to move to the bioconductor list for specific guidance >> on this type of dataset. >> >> >> On Thu, Dec 27, 2018 at 3:28 PM Spencer Brackett < >> spbracket...@saintjosephhs.com> wrote: >> >>> Mr. Calboli, >>> >>> After beginning to unpack the GBM file you sent me via directly importing >>> it unit my console, I received the following: >>> >>> View(GBM_PEXP.tsv) >>> >>> **Note that I named the file GBM_PEXP.tsv)** >>> >>> Upon downloading, my script now contains a 2 by 2 table, with the x >>> column still containing encoded script. As for my Data summary to the >>> right, this new file reports that 2 objects are acting upon 1 variable. >>> How should I proceed? >>> >>> -Spencer >>> >>> On Thu, Dec 27, 2018 at 3:12 PM Federico Calboli < >>> federico.calb...@kuleuven.be> wrote: >>> >>> > Unpack these files. >>> > >>> > F >>> > >>> > >>> >>> [[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.