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Cancer Data for process

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
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written by landscape95 landscape95

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

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written by GenoMax GenoMax

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!

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written by landscape95 landscape95

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

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written by poisonAlien poisonAlien

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!

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written by landscape95 landscape95

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!

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written by landscape95 landscape95

Do you want to give us that warning also?

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written by Michael Dondrup Michael Dondrup

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
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updated by Michael Dondrup Michael Dondrup • written by landscape95 landscape95

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.

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written by Michael Dondrup Michael Dondrup

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