User: salvocomplicazioni1

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Posts by salvocomplicazioni1

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Comment: C: Issue with TCGAbiolinks package.
... Yes, TCGAbiolinks version 2.10.3 fix the issue. ...
written 4 months ago by salvocomplicazioni10
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Comment: C: Issue with TCGAbiolinks package.
... I found in readGISTIC function: ``` else if (grepl("Copy Number Variation", query$data.category, ignore.case = TRUE)) { if (query$data.type == "Gene Level Copy Number Scores") { data <- readGISTIC(files, res$results[[1]]$cases) } else { data <- readCopyNumberVariat ...
written 4 months ago by salvocomplicazioni10
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Comment: C: Issue with TCGAbiolinks package.
... ``` > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.5 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 locale: [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C ...
written 4 months ago by salvocomplicazioni10
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Issue with TCGAbiolinks package.
... I'm trying to download copy number variation file with TCGAbiolinks package and following code: ``` library(TCGAbiolinks) Tumor <- c("BLCA) query <- GDCquery(project = paste("TCGA-",Tumor, sep = ""), data.category = "Copy Number Variation", data.type = "Gen ...
tcga gdcprepare written 4 months ago by salvocomplicazioni10
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Problems with Edge R normalization in same sample but using different ref genomes.
... Hi Starting from Rna-seq data raw counts, I used TCGAanalyze_Normalization function based on edger, so i obtained normalized count. If i perform same analysis on two data type (GRCh37 and GRCh38) i obtain completely different normalized counts. Results are these: GRCh38   Sample1 ...
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TCGA-biolink: GRCH38 RNA-seq, normalized counts matrix, Converting ensemble gene name into common gene name
... I'm trying to analyze TCGA RNA-seq data, so i used TCGAbiolinks, I arrived at normalization data step and i obtained normalized counts matrix, How can I change Ensemble gene name into common gene name? ...
annotation grch38 tcgabiolinks written 20 months ago by salvocomplicazioni10 • updated 20 months ago by tiagochst110

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