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Question: Extract gene expression values from GDCprepare object
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gravatar for enigmargs
9 months ago by
enigmargs0
enigmargs0 wrote:

Hello, I am trying to download gene expressions values from TCGA-GBM project from GDC using TCGAbiolinks using the example code below;

query <- GDCquery(project = "TCGA-GBM", legacy = TRUE,
        data.category = "Gene expression", data.type = "Gene expression quantification",
        platform = "Illumina HiSeq", file.type = "normalized_results", experimental.strategy = "RNA-Seq")

GDCdownload(query); GDCprepare(query, save=T)

But, I am unable to save the object from GDCprepare. Should the object from GDCprepare result in a dataframe? (It's not a dataframe when I checked it). If so how to access the gene expression values within them? Is it possible to extract only gene expression and patient ID from S4 object resulting from GDCprepare

Any help is much appreciated.

 

ADD COMMENTlink modified 8 months ago by tiagochst90 • written 9 months ago by enigmargs0
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gravatar for tiagochst
8 months ago by
tiagochst90
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
tiagochst90 wrote:

Hi,

The default GDCprepare output is a SummarizedExperiment (SE) object, but you can also set to output the data frame.

The main difference is the the SE  has gene information (start, end and others) and sample information.

There are some examples here: https://www.bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/download_prepare.html

Best regards,

Tiago

ADD COMMENTlink written 8 months ago by tiagochst90
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