GDCquery - warning

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2.0 years ago

Negatyvna • 0

Hi, I have a question. Is it possible to somehow remove the warning?

query1 <- GDCquery( project = "TCGA-COAD", data.category = "Simple Nucleotide Variation", data.type = "Masked Somatic Mutation", legacy=F)
Warning: There are more than one file for the same case. Please verify query results. You can use the command View(getResults(query)) in rstudio
ooo Check if there results for the query

maf GDCquery • 915 views

ADD COMMENT • link 2.0 years ago by Negatyvna • 0

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If you wish to just "somehow remove the warning", use suppressWarnings. If you want to address the underlying problem (which is what you should be doing), follow the recommendations in the message and look at getResults(query) and see if you can be more specific about the dataset you want.

ADD REPLY • link 2.0 years ago by Ram 43k

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I tried all the options and still have the same error, does anyone have any idea?

ADD REPLY • link 2.0 years ago by Negatyvna • 0

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What are "all the options" that you tried?

ADD REPLY • link 2.0 years ago by Ram 43k

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I tried to set up workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking", experimental strategy are the same in the sample, I tried to look for duplicated samples, e.g. the id showed nothing to me.

ADD REPLY • link 2.0 years ago by Negatyvna • 0

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