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mksamur / RTCGAToolbox

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getFirehoseData silent defaults #11

Closed aaronwolen closed 7 years ago

aaronwolen commented 9 years ago

There are a couple of cases where getFirehoseData() silently chooses among several candidate files for a particular data type.

First, when data is available from both fresh and FFPE samples getFirehoseData() defaults to the non-FFPE file. I think that makes sense but should probably be documented somewhere.

Second, and more problematic, when data is available from both hi-seq and genome analyzer sequencers, the latter is selected. For example,

getFirehoseData("COAD", getFirehoseRunningDates(1), RNAseq2_Gene_Norm = TRUE)

downloads and imports data from gdac.broadinstitute.org_COAD.Merge_rnaseqv2__**illuminaga**_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gz, even though gdac.broadinstitute.org_COAD.Merge_rnaseqv2__**illuminahiseq**_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2015040200.0.0.tar.gz is also available.

Is that intentional?

mksamur commented 9 years ago

that is actually not intentional let me think about it