Admin: Marcel Ramos

gravatar for Marcel Ramos
Marcel Ramos ♦♦ 140
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5 days, 21 hours ago
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3 years, 4 months ago
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Posts by Marcel Ramos

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Retrieve accurate tumor stage data with TCGAbiolinks
... Hi Benjamin, It would be good to have Tiago Silva's input on this. It seems like, at least for this case, the curation process considered the TNM stages and coded for Stage IV Here are a few other resources that you can use to check these variables (many of which yield NA for pathologic_stage): Geno ...
written 5 weeks ago by Marcel Ramos ♦♦ 140
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Answer: A: Error while getFirehoseData of RTCGAToolbox package
... Hi Ankita, I was unable to reproduce the error. I suspect that it may have something to do with your internet connection.  Please check your connection settings and make sure that a firewall or VPN is not preventing you from accessing the remote file.  There are other known issues for users of Wi ...
written 10 weeks ago by Marcel Ramos ♦♦ 140
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Comment: C: R_Granges_adding merged Metadata columns
... Hi Melissa, Without a reproducible example, there is not much specific help that fellow Bioconductor users can provide. If you have the ranges of those variants that have been merged, you can use findOverlaps to find the overlapping ranges in the original GRanges that correspond to those variant acc ...
written 10 weeks ago by Marcel Ramos ♦♦ 140
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Comment: C: Error while uploading Bioconductor packages - R Shiny
... Hi Lloyd,  Thanks for posting a solution!  Best regards, Marcel  ...
written 12 weeks ago by Marcel Ramos ♦♦ 140
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Answer: A: Can i add an experiment to an existing MultiAssayExperiment?
... Hi Mario, Thank you for posting on the support site. Yes, there is a method to add an experiment using the c function. This works quite easily if this experiment has the same sample composition and order as another experiment. You can then use: c(mymultiassay, newExpAssay = tcia, mapFrom = 1L) Ot ...
written 3 months ago by Marcel Ramos ♦♦ 140
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Comment: C: Inconsistent Warning: GRanges out of bounds
... Hi znl207, In order for anyone to provide assistance, please post a fully reproducible and minimal example of the issue. What I see from the output, it doesn't look like an error but more of a warning. It could be related to a number of issues including the integrity of the data. One option you coul ...
written 4 months ago by Marcel Ramos ♦♦ 140
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Answer: A: Error when subsetting a RaggedExperiment by GenomicRanges
... Hi Carlos, Thank you for your report. This is indeed a bug in the subsetByOverlaps,RaggedExperiment,Vector-method. This was fixed in version 1.2.4 in release and 1.3.7  in devel. Regards, Marcel ...
written 6 months ago by Marcel Ramos ♦♦ 140
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Answer: A: Error when prepare the TCGAdata
... Hi Michael Wang, This seems to be a memory issue. Methylation data is quite large and may exhaust your memory resources when trying to merge the various files that you've downloaded. The total size of the files is ~10.8 Gb. Downloading data for project TCGA-LUAD GDCdownload will download 507 files ...
written 6 months ago by Marcel Ramos ♦♦ 140
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Comment: C: GenomicRanges_RaggedExperiment Error in as background, class mcol no method or d
... Updates: This has been fixed in `1.2.3` in release and `1.3.5` in devel.  Marcel ...
written 6 months ago by Marcel Ramos ♦♦ 140
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Answer: A: GenomicRanges_RaggedExperiment Error in as background, class mcol no method or d
... Hi Taran,  Apologies for the late response. I have looked at the issue and we're working on a fix.  The reason you're getting an error in that call is that you are introducing an "score" column of type `factor`.  The quick fix for this issue is to coerce the "score" column to character and rerun th ...
written 6 months ago by Marcel Ramos ♦♦ 140

Latest awards to Marcel Ramos

Scholar 12 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data
Scholar 14 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data
Scholar 14 months ago, created an answer that has been accepted. For A: Classes and methods for working with segmented copy number data

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