Question: Cancer Data for process
0
gravatar for landscape95
2.3 years ago by
landscape95160
landscape95160 wrote:

I am doing projects in Cancer, now I need to download the data of Breast cancer such as miRNA, mRNA (separate them into Transcription factors and normal mRNAs), DNA methylation, somatic mutation, and clinical data. We use Bioconductor, (TCGAbiolinks), Firehose. How can I do? Thanks in advance!

cancer • 867 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by landscape95160

If you already know about/use those programs what else do you want to know how to do?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax70k

I got a warning when I use this command "query <- GDCquery(project = "TCGA-BRCA", data.category = "DNA Methylation", data.type = "Methylation Beta Value")" Could you please help me how to solve it? Thanks in advance!

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by landscape95160

Did you read TCGAbiolinks vignette ? Its pretty well documented for all the things that you're asking.

ADD REPLYlink written 2.3 years ago by poisonAlien2.8k

I got a warning when I use this command "query <- GDCquery(project = "TCGA-BRCA", data.category = "DNA Methylation", data.type = "Methylation Beta Value")" Could you please help me how to solve it? Thanks in advance!

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by landscape95160

I got a warning when I use this command "query <- GDCquery(project = "TCGA-BRCA", data.category = "DNA Methylation", data.type = "Methylation Beta Value")" Could you please help me how to solve it? Thanks in advance!

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by landscape95160

Do you want to give us that warning also?

ADD REPLYlink written 2.3 years ago by Michael Dondrup46k

Here it is, but the type of data is only in "Methylation Beta Value"

|sort(harmonized.data.type)        | |:---------------------------------| |Biospecimen Supplement           | 
|Clinical Supplement               | |Copy Number Segment            | |Gene Expression Quantification   
| |Isoform Expression Quantification | |Masked Copy Number Segment        | |Masked Somatic Mutation           | |miRNA Expression Quantification   | 
Error in checkDataTypeInput(legacy = legacy, data.type = data.type) :    Please set a data.type argument from the column harmonized.data.type above
ADD REPLYlink modified 2.3 years ago by Michael Dondrup46k • written 2.3 years ago by landscape95160
1

I don't know this package, but if I understand correctly, you need to select one of harmonized.data.type for the data.type argument. But you you selected "Methylation Beta Value", which is possibly not available.

ADD REPLYlink written 2.3 years ago by Michael Dondrup46k
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