Cancer Data for process

Question

[landscape95]

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!

[GenoMax]

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

[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!

[poisonAlien]

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

[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!

[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!

[Michael]

Do you want to give us that warning also?

[landscape95]

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

[Michael]

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.