Hello, I'm starting in a project involving the analysis of microarray gene expression data and I began with TCGAbiolinks. I have downloaded the data succesfully from TCGA and now I'm trying to prepare the data with the function TCGAprepare, for probe-level microarrays is fine (if I put SummarizedExperiment as False, otherwise give me an error), but for the platforms of oligonucleotide and exon microarrays it doesn't return nothing (an empthy object). Is because the package isn't intended to deal with this kind of data?, or is that I'm not doing things ok?
I added the platforms, it is in github it will be soon in Bioconductor.
Yes, the type argument was more RNA-seq oriented. But as other platforms has sometimes more than one data type we are trying to provide both for the users. We need to improve/update the vignette.
What I understood from the question is how I linked the experiment (files with data) with the barcode (I'm sorry if I got it wrong). To map the barcodes to the experiments there are three types of situations:
- Barcode in the filename
- Uuid in the filenames, then we map the uuid to tcga using TCGA api
- sdrf files in the mage folder: each experiment normally has a folder with the metada information that maps the file to the TCGAbarcode. Example for HuEx-1_0-st-v2
More or less these cases can be seen in this code
In TCGAprepare we only read the data, no normalization is done. If further steps needs to be made, it is up to the user.
Also, there is another database called FIREHOSE https://gdac.broadinstitute.org/. Firehose got TCGA data and sometimes they do some processing steps, you can also download the data from there with other packages (TCGA2STAT, RTCGAtoolbox).