User: mathias.heydt

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Posts by mathias.heydt

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Comment: C: EPIC array annotation
... I was trying to find out all options about annotating my data as well - I've got TCGA data that is not annotated yet. I was unsure about the manifest files some packages used, but did not know how to proceed. Your script seems very helpful, but is it solving your problem? I haven't found the time ...
written 10 weeks ago by mathias.heydt80
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Answer: A: TCGAbiolinks download error
... You need to add your data.type, that's all ;): bio_query <- GDCquery(project = "TCGA-PRAD", data.category ="Biospecimen", data.type="Biospecimen Supplement") Basically, if you specify Biospecimen in your data category in the [TCGA repository][1], you'll see that it contains two datatypes. Y ...
written 10 weeks ago by mathias.heydt80
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How to avoid annotating multiple genes to a single CpG locus?
... I am downloading TCGA DNA methylation data using TCGAbiolinks. The rowData() function output looks a bit messy; all ensembl ids with which a cpg overlaps are joined together in one cell, just like the hgnc symbols and gene types. I want to just provide one column with protein coding gene hgnc symbo ...
tcgabiolinks R biomart dna annotation written 10 weeks ago by mathias.heydt80 • updated 10 weeks ago by Mike Smith820
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Is there public (DNA methylation) data on circulating cell-free DNA - why not?
... In the near future, I will have to deal with circulating cell-free DNA in the context of finding cancer biomarkers - I have read up on methylation, biomarkers, cancer, though I must admit I haven't read too much about cfDNA yet. In this context, it seems strange that I can't find (450k) methylation ...
epigenetics circulating cell-free dna biomarker written 3 months ago by mathias.heydt80 • updated 3 months ago by Kevin Blighe26k
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Comment: C: TCGA calling pipeline query
... Have you tried looking [here][1]? I found it difficult to find my way to all of these pages, but maybe your answer is in there. [1]: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/#somatic-variant-calling-workflow ...
written 4 months ago by mathias.heydt80
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Answer: A: Differential methylation analysis
... If you have already downloaded your data, you can also make use of the ChAMP package. https://bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.html It makes use of the limma package, so you'd use linear models instead of regular t-tests to find DMPs. [This section][1] show you ...
written 4 months ago by mathias.heydt80
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Comment: C: Data Discrepency from TCGA-GDC portal and GDC firehose
... You are using TCGAbiolinks already, aren't you then also retrieving the full ids for the clinical data? This should help you: I assume you're starting with: query <- GDCquery("yourquery") Then just type: getResults(query, cols = c("cases", "tissue.definition")) ...
written 4 months ago by mathias.heydt80
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Comment: C: TCGABioLinks how to set Sample conditions?
... You're doing something totally different from the example, and different from your first question anyway. The MAE is a separate class, and in the example, they create it using summarizedExperiment class objects (lusc.exp and lusc.met) I'm not using these classes, so I can't look into it for you, but ...
written 5 months ago by mathias.heydt80
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Comment: C: TCGABioLinks how to set Sample conditions?
... Yeah, like I said in my answer, if you know the barcodes of your samples in set A and set B, you can just specify them; In the example they specify their sets with the TCGAquery_samples function. You don't need to do that. Just list the barcodes directly. dataSmTP is just a variable name, so you can ...
written 5 months ago by mathias.heydt80
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Comment: C: help with GDCprepare
... I was able to download and prepare it. Could be the biomart servers were down, so try again?. And if it still isn't working, you could consider downloading the developer version of tcgabiolinks if you haven't done that. Alternatively, it could be due to the fact that you're asking legacy data. Do yo ...
written 5 months ago by mathias.heydt80

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