COAD samples do not have any normals

[LiNk-NY]

There appears to be a bug in this line: https://github.com/LiNk-NY/RTCGAToolbox/blob/master/R/getFirehoseData.R#L352

where earlier data from one file gets replaced in the subsequent loop.

[Yazhouhe]

Hi has this been fixed yet? I found it happens with other samples as well. Seems only the BRCA works well with normals.

[LiNk-NY]

Hi @Yazhouhe I will look into it. Thanks for the reminder. Best, Marcel

[LiNk-NY]

Hi @Yazhouhe It should have been fixed some time ago. See this:

library(RTCGAToolbox)
coad <- getFirehoseData("COAD", RNASeq2GeneNorm = TRUE, clinical = FALSE)
#> gdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0.tar.gzgdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0.tar.gz
#> gdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0
#> RNAseq2 data will be imported! This may take a while!
#> Start: 2019-08-03 23:19:37
#> Done: 2019-08-03 23:19:38
#> gdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0
#> RNAseq2 data will be imported! This may take a while!
#> Start: 2019-08-03 23:19:47
#> Done: 2019-08-03 23:19:50
getData(coad, "RNASeq2GeneNorm")
#> [[1]]
#> gdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminaga_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0.tar.gz
#> FirehoseCGHArray object, dim: 20501  191
#> 
#> [[2]]
#> gdac.broadinstitute.org_COAD.Merge_rnaseqv2__illuminahiseq_rnaseqv2__unc_edu__Level_3__RSEM_genes_normalized__data.Level_3.2016012800.0.0.tar.gz
#> FirehoseCGHArray object, dim: 20501  328
packageVersion("RTCGAToolbox")
#> [1] '2.15.4'

^{Created on 2019-08-03 by the reprex package (v0.3.0)}