User: Fernando

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Fernando0
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Cuba
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Posts by Fernando

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Comment: C: Using TCGAbiolinks for exon and oligonucleotide level microarray
... Thanks tiagochst, for your answer (which was very fast) and the changes to the package for make me the life easier. You got it right, that was exactly what I was asking. I know that the package (from what I read) is not intended (at least for now) to do normalization to all platforms, but in fact I ...
written 12 months ago by Fernando0
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Comment: C: Using TCGAbiolinks for exon and oligonucleotide level microarray
... 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 mo ...
written 12 months ago by Fernando0
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Comment: C: Using TCGAbiolinks for exon and oligonucleotide level microarray
... 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 ...
written 12 months ago by Fernando0
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Using TCGAbiolinks for exon and oligonucleotide level microarray
... 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 SummarizedExp ...
microarray tcga exons tcgabiolinks oligonucleotide written 12 months ago by Fernando0 • updated 12 months ago by tiagochst80
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normalizing gene expression data with TCGAbiolinks
... I want to work with data of microarray gene expression, and after read the article of TCGAbiolinks and the extended information of the functions of the package, it seems that the package don't have a function to normalize the data of microarray, because its function TCGAanalyze Normalization appears ...
rnaseq microarray tcgabiolinks written 12 months ago by Fernando0
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Comment: C: TCGAbiolinks data download problem
... Thank for your answer, it must be that. I tried later to download another archives of level 2 and there wasn't any problem. ...
written 12 months ago by Fernando0
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TCGAbiolinks data download problem
... Hello I'm new with Bioconductor and microarray analysis. I am trying to download data with the function TCGAdownload, and first I had this error: Error in curl::curl_download(input, tt, mode = "wb", quiet = !showProgress) : Timeout was reached Then, for what I have read (https://support.biocon ...
microarray cancer bioconductor tcgabiolinks written 13 months ago by Fernando0
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Comment: C: TCGAbiolinks data download error
... Hello, I have the same problem, but I don't understand the answer suggested by tiagochst. Could you give me a more extended explanation? ...
written 13 months ago by Fernando0

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