lusc_tcga_pub, prad_tcga_pub,

[asamedy]

Error in .generateMap(pData, experiments) : no way to map pData to ExperimentList http://www.cbioportal.org/study?id=lusc_tcga#summary http://www.cbioportal.org/study?id=prad_tcga#summary

[LiNk-NY]

Hi Andy, @asamedy This is common in TCGA data because Patient IDs are shorter than Sample IDs but share a common set of identifying information. Try using

TCGAutils::generateMap(colData, experiments, TCGAutils::TCGAbarcode)

[asamedy]

Thanks for the tip Marcel. Will try that.

On Tue, May 16, 2017 at 3:50 PM, Marcel Ramos notifications@github.com wrote:

Hi Andy, @asamedy https://github.com/asamedy This is common in TCGA data because Patient IDs are shorter than Sample IDs but share a common set of identifying information. Try using

.generateMap(colData, experiments, TCGAutils::TCGAbarcode)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/waldronlab/MultiAssayExperimentData/issues/2#issuecomment-301895615, or mute the thread https://github.com/notifications/unsubscribe-auth/AM68n_a017ShxSuoKuaaepbJG-WDV_tYks5r6f4TgaJpZM4Nc6UI .

[LiNk-NY]

@lwaldron I had a look at this and whoever uploaded this study dataset, mangled the names:

head(rownames(coldata))
[1] "LUSC-18-3406" "LUSC-18-3407" "LUSC-18-3408" "LUSC-18-3409" "LUSC-18-3410"
[6] "LUSC-18-3411"

They will never match up when colnames(exptlist) is something like:

CharacterList of length 11
[["CNA"]] TCGA-18-3406 TCGA-18-3408 TCGA-18-3410 ... TCGA-70-6723 TCGA-85-6560

I will replace LUSC with TCGA.

Regards, Marcel

[LiNk-NY]

I've added a helper to remove any instances of LUSC or [A-Z]{4} that are not TCGA and replace them with TCGA.

[LiNk-NY]

Oops, wrong commit noted.