error in `rearrange` method for GBM object

[lwaldron]

e.g.:

> gbm <- readRDS("gbmMAEO.rds")
> gbm2 <- gbm["EGFR", , c("RNASeq2GeneNorm", "mRNAArray", "RPPAArray", "gistica")]
> gbm2
A MultiAssayExperiment object of 4 listed
 experiments with user-defined names and respective classes. 
 Containing an ExperimentList class object of length 4: 
 [1] RNASeq2GeneNorm: ExpressionSet with 1 rows and 166 columns 
 [2] mRNAArray: ExpressionSet with 1 rows and 528 columns 
 [3] RPPAArray: ExpressionSet with 1 rows and 244 columns 
 [4] gistica: SummarizedExperiment with 1 rows and 577 columns 
To access: 
 experiments() - to obtain the ExperimentList instance 
 pData() - for the primary/phenotype DataFrame 
 sampleMap() - for the sample availability DataFrame 
 metadata() - for the metadata object of ANY class 
See also: subsetByAssay(), subsetByRow(), subsetByColumn()
> rearrange(gbm2)
Error: subscript contains invalid names
> 

[LiNk-NY]

Can you send me the gbm2 object as an RDS? I can debug it.

[lwaldron]

Github allows .zip but not .rda, so here is a .rda.zip:

gbm2.rda.zip

[lwaldron]

Actually I may as well give you another object that also has the mutations and gistic, for slightly more of a challenge:

gbm3 <- gbm["EGFR", , ] gbm3.rda.zip

[LiNk-NY]

I fixed part of this in 111ae41058713d6e856d18277636d58a0cec4180

[LiNk-NY]

It looks like the data in gbm3[["Mutations]] is not numeric and is missing. See: lapply(gbm3[["Mutations"]], function(x) mcols(x)["Score"]) I'd have to check to see what happened with the data at some point in the pipeline.

[lwaldron]

I should check first that it wasn't bad subsetting...

On Feb 2, 2017 6:01 PM, "Marcel Ramos" notifications@github.com wrote:

It looks like the data in gbm3[["Mutations]] is not numeric and is missing. See: lapply(gbm3[["Mutations"]], function(x) mcols(x)["Score"]) I'd have to check to see what happened with the data at some point in the pipeline.

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[LiNk-NY]

The subsetting works but the data in mcols are blank characters.

[lwaldron]

rearrange() has been deprecated by longFormat() and wideFormat(). These work fine on gbm3 except for the Mutations slot, but this is an issue with the RRA object or with reducing it. Revisit this with documentation when curatedTCGAData is ready.

[LiNk-NY]

This can be revisited and posted in the curatedTCGAData issues page if need be. https://github.com/waldronlab/curatedTCGAData