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?
Hi Fernando, we don't have all platforms in TCGAprepare. Do you have an example of these two platforms?
There is a list in the vignette, but I'm not sure which one it is. I'll try to add them asap.
Hello, thanks for answer me again. For example, for exon microarrays, I did
TCGAquery(tumor = "gbm", platform = "HuEx-1_0-st-v2", level=3) (which works perfectly as the TCGAdownload function)
but I get a NULL object when I use TCGAprepare. But it isn't a big trouble, because I can try to make the matrix of the experiments. What I don't understand is something in the downloaded files: the numbers of barcodes of the experiments of a .txt file are smaller than the number of signal measures in that file, could you explain me why this happens?
Yes, there was no code for this platform ("HuEx-1_0-st-v2)
I just added the code in the github repository (https://github.com/BioinformaticsFMRP/TCGAbiolinks)
I'll add to bioconductor soon.
Thank you very much, tiagochst. But well, now that we are asking... could you please do something too with this platforms:
HG-CGH-244A, HG-CGH-415k_G4124A, CGH-1x1M_G4447A ?
I see, that you add also the option of gene in type, which wasn't there, because in here and here the package seems always more oriented to RNA-seq data.
And for a last thing (this maybe is too much, but who could say?), could you recommend me some bibliography to understand better the underlying methods behind the package?, this is for learn also how to do the things (for example, I don't know how works the TCGAprepare function to join the exon microarrays experiments with their respective TCGA codes (I know that you have covered, but I don't understand how)), I am very very new in this subject.