pradMAEO-RTCGAToolbox function definition

[RM-SCB]

In the function definition of pradMAEO-RTCGAToolbox, should "serialPath" not be "serialpath"? Cheers

[LiNk-NY]

Thanks for catching that. Fixed. Regards, Marcel

[RM-SCB]

Hi Marcel,

Thanks for this. How updated are the files in the .rds objects? I found different total number of patients comparing the .rds file for PRAD compared to what’s available on cBioportal for example.

Many thanks,

Renaud

From: Marcel Ramos notifications@github.com<mailto:notifications@github.com> Reply-To: waldronlab/MultiAssayExperiment reply@reply.github.com<mailto:reply@reply.github.com> Date: Friday, 16 June 2017 at 23:52 To: waldronlab/MultiAssayExperiment MultiAssayExperiment@noreply.github.com<mailto:MultiAssayExperiment@noreply.github.com> Cc: Renaud Mevel Renaud.Mevel@cruk.manchester.ac.uk<mailto:Renaud.Mevel@cruk.manchester.ac.uk>, Author author@noreply.github.com<mailto:author@noreply.github.com> Subject: Re: [waldronlab/MultiAssayExperiment] pradMAEO-RTCGAToolbox function definition (#207)

Thanks for catching that. Fixed. Regards, Marcel

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[LiNk-NY]

Hi Renaud, The serialized data is coming from the RTCGAToolbox where we have the last TCGA run date of Jan. 28, 2016. It may be possible that some patients were dropped if they had no data at all in the PRAD dataset. Throughout our pipeline, we strive to not remove any patients unnecessarily.

We are also in the process of making cBioPortal data available as MultiAssayExperiment objects.

We're happy to hear about any differences you've found between datasets. Thanks!

Regards, Marcel