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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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TCGAanalyze_Normalization #38

Open SonicHedgehogSHH opened 8 years ago

SonicHedgehogSHH commented 8 years ago

Hi! I would like your help. I have used GDCquery and then GDCdownload to download the TCGA data. After that I used data <- GDCprepare(query) successfully but I get error messages when I try TCGAanalyze_Normalization. I use TCGA_Normalization(tabDF=data, geneInfo=geneInfo). Why is that? Could you please provide me with the missing steps? Best wishes

tiagochst commented 8 years ago

Hi, Please, could you share your code so we can reproduce the problem and the version of the package you are using? Thanks

tiagochst commented 8 years ago

The documentation is wrong it says it will receive a matrix, but the input is a summarizedExperiemnt.

Does it work? dataNorm <- TCGAanalyze_Normalization(tabDF=exp, geneInfo=genes.info, method="gcContent")

@torongs82 Could you update the manual?

SonicHedgehogSHH commented 8 years ago

Hi! Thanks for the reply! I used the code u just provided but the same error message comes. I actually moved on with the filtering step (without using the normalization step) and it just worked..Is this wrong?

tiagochst commented 8 years ago

Anotnio (@torongs82) wrote this pipeline. He is the best person to answer it.

torongs82 commented 7 years ago

Hi @SonicHedgehogSHH,

I apologise for this delay in my writing. Of course the filtering step in TCGAanalyze_Filtering is working but let's say that is better to preprocess the data and then normalize it before going beyond downstream analysis. For this reason you need only to run two step as showed in our vignette:

dataPrep <- TCGAanalyze_Preprocessing(object = brca.exp, cor.cut = 0.6)

dataNorm <- TCGAanalyze_Normalization(tabDF = dataPrep, geneInfo = geneInfo, method = "gcContent")

where in particular 'brca.exp' has a class of RangedSummarizedExperiment output from TCGAprepare and dataPrep is a numeric matrix as output from TCGAanalyze_Normalization.

If you need any informations you can write us. Best, Antonio.